Evolutionary fate of the androgen receptor-signaling pathway in ray

Evolutionary fate of the androgen receptor-signaling pathway in ray-finned fishes with a special focus on cichlids

Thibault Lorin*§, Walter Salzburger§, Astrid Böhne§1 * ENS (Ecole Normale Supérieure de Lyon), Lyon Cedex 07, France; §

Zoological Institute, Department of Environmental Sciences, University of

Basel, 4051 Basel, Switzerland

1

Corresponding author: Astrid Böhne, Zoological Institute, Department of

Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland, +41 61 267 03 01, [email protected]

DOI: 10.1534/g3.115.020685

Figure S1 Maximum-likelihood single gene phylogenetic reconstructions for genes of the AR signaling pathway in ray-finned fishes using PhyML 3.1 (Guindon et al. 2010) under the GTR + gamma + I model, with 1,000 bootstrap replicates.

2 SI

T. Lorin, W. Salzburger & A. Böhne

Figure S1 0.05 NM_001281801.1 932 ENSAMXG00000009230

961

ENSAMXG00000012355

GI_548423349 702 619

GI_498935125

Gene: akt1 GI_554812288 1000 GI_542229192

583

GI_583981523

ENSPFOG00000010125 1000 ENSXMAG00000006673 388

522 ENSORLG00000017024

ENSTRUG00000013476 983 999 ENSTNIG00000019495

ENSGACG00000006298

ENSLOCG00000012762

3 SI


Figure S1 0.1 ENSPFOG00000006490

1000

ENSXMAG00000002896

989

ENSORLG00000008220 671

782

GI_545793521

1000 GI_555943746

98 451

GI_499025148 GI_583972812

1000

ENSONIG00000017538 1000

ENSTNIG00000015783 1000

ENSTRUG00000005373

999

ENSGACG00000018525 ENSAMXG00000013256 956

GI_548397957

1000

GI_499011353

882

GI_555943801

1000

Gene: ar

GI_584009291 ENSONIG00000012854

794 1000

ENSPFOG00000019378 ENSXMAG00000012307

1000

854 ENSORLG00000009520 ENSGACG00000020332 747

976

ENSTNIG00000011826 1000

ENSTRUG00000012421

ENSDARG00000067976 999

ENSAMXG00000011395 ENSLOCG00000014680

4 SI



1000

ENSXMAG00000010716

919

ENSORLG00000004410 571

566

982

GI_548435329 GI_499018427

999 GI_554870576 1000

GI_584001874

1000

ENSONIG00000006764 ENSTRUG00000013351

1000 1000

ENSTNIG00000009659 788 ENSGACG00000007244 ENSDARG00000101710 1000

ENSAMXG00000020237 ENSDARG00000101891

1000

ENSAMXG00000013606 952 1000

GI_499027400 GI_548538463

1000 GI_554835101 983

1000

GI_584000591 ENSONIG00000007618

999

ENSPFOG00000002208 1000

ENSXMAG00000012041

1000 1000

ENSTRUG00000012325 ENSTNIG00000004670

876 ENSGACG00000007627 ENSLOCG00000003798

5 SI


Gene: arid1a

Figure S1 0.1 ENSAMXG00000015282

ENSPFOG00000004731 1000 ENSXMAG00000009949

994

ENSORLG00000004585

Gene: brca1

GI_548541303 769

994

997

GI_499033693

1000 GI_554835497

804 1000

GI_583992196

ENSONIG00000016326

1000 ENSGACG00000006381

ENSTRUG00000009091 1000 ENSTNIG00000010246

ENSLOCG00000011391

6 SI


Figure S1 0.05 ENSPFOG00000014440 1000 ENSXMAG00000014453

GI_499007024 193 184 981

997

GI_554856484

GI_548521455

Gene: cav1 767

GI_583973968

998

ENSONIG00000003896

ENSORLG00000019746 711 400 ENSGACG00000009201

ENSTRUG00000017112 431 ENSTNIG00000016057

ENSAMXG00000011618 953 ENSDARG00000052004

ENSLOCG00000015597

7 SI


Figure S1 0.1 ENSTRUG00000001296 ENSTRUG00000017625 ENSTRUG00000001857

1000 575 341 474

85

973

ENSTRUG00000001834

Gene: ccne1 ENSTRUG00000000353

ENSTRUG00000000222

ENSTRUG00000000484 ENSTNIG00000006196 ENSPFOG00000011801 1000 ENSXMAG00000001005 1000 519 359

GI_499030053

988 GI_554826914 995 GI_548348207

450

GI_584015275

1000

ENSONIG00000003504 618 ENSORLG00000015511 ENSGACG00000012549 ENSDARG00000098622 832 ENSAMXG00000002929 ENSLOCG00000005671

SI


Figure S1 0.1

GI_545793478 660

GI_494461779

979 GI_545786543 954

GI_573898313

580

ENSONIG00000016914 ENSGACG00000012448

727

ENSTRUG00000013411 946

995

ENSTNIG00000012549 ENSPFOG00000005335

994 619

ENSORLG00000013756 889 ENSXMAG00000016228 ENSAMXG00000019820 ENSPFOG00000004608

992

ENSXMAG00000008839

910 543

501

ENSGACG00000010913 ENSTNIG00000007372

965

ENSORLG00000012048

793 ENSTRUG00000000167 560

932

545

ENSONIG00000020235

GI_554846439 GI_499018345

GI_584010624

915

GI_548348712 ENSAMXG00000003583 ENSDARG00000044573 ENSLOCG00000001073

SI


Gene: cdc42

Figure S1 0.1 GI_554874678 901 GI_548339440 909

Gene: cdk7 867

GI_498955997

1000

GI_583977761

513

ENSONIG00000013709

ENSORLG00000008836

835

ENSPFOG00000017422 812

997 ENSXMAG00000007316

1000

ENSGACG00000009848

ENSTNIG00000015407 990 ENSTRUG00000010233

ENSAMXG00000008454 927 ENSDARG00000051916

ENSLOCG00000006117

SI


Figure S1 0.1 GI_554852342 595

GI_548490653 609

Gene: cfl1l GI_584024814

1000

ENSONIG00000010009

860 ENSXMAG00000006139 999

ENSPFOG00000017145 1000

807

ENSORLG00000011865

ENSGACG00000004750

ENSDARG00000012972

923 ENSAMXG00000007837

ENSLOCG00000015680

SI


Figure S1 0.1 ENSTRUG00000003520 1000 ENSTNIG00000019094

Gene: ctnnb1 ENSPFOG00000018568 1000 ENSXMAG00000008710

418

ENSORLG00000005845

1000

GI_499034959 696

634

GI_554880769 969

GI_548426098 791 378 733 1000

ENSONIG00000007226

GI_583999804

ENSGACG00000006037

ENSAMXG00000000198

ENSDARG00000014571

ENSLOCG00000001383

SI


Figure S1 0.1 ENSTNIG00000005315 1000 ENSTNIG00000018185

999

ENSTRUG00000003811

511

ENSGACG00000001844

GI_554886315 982

396

996

Gene: daxx GI_548490874

998 GI_499044186

595 1000

GI_573898112

ENSONIG00000008401

894

ENSPFOG00000001776 1000 ENSXMAG00000007090

ENSORLG00000006837

ENSDARG00000000729 881 ENSAMXG00000014180

ENSLOCG00000000498

3 SI


Figure S1 0.1 GI_548348922 465

604

Gene: dnaja1

GI_554873916

664 GI_498979425

1000

526

GI_583983886

ENSONIG00000014539

ENSGACG00000017879

1000

ENSPFOG00000005099 1000

1000

ENSPFOG00000004920

ENSXMAG00000005855 466

ENSORLG00000006260

ENSAMXG00000010757 834 ENSDARG00000030972

ENSLOCG00000011564

4 SI


Figure S1

997

ENSTNIG00000000023

1000

Gene: egfr

0.1 ENSTNIG00000013553

1000

ENSTNIG00000013552

741

ENSTRUG00000017446 ENSGACG00000018079 ENSORLG00000003577

1000

508 ENSPFOG00000005185 1000

ENSXMAG00000008804 821 GI_545785452

425

989 GI_548511931

906

989 GI_499050178 GI_584029670

1000

ENSONIG00000017327 ENSAMXG00000015959 ENSPFOG00000008848

1000

ENSXMAG00000016482

679

ENSORLG00000017692 535

565

GI_548422483

1000 GI_554803235 995

1000

1000

GI_498945991 GI_583994068 ENSONIG00000009358

1000

ENSTRUG00000011834 ENSTNIG00000014840

811

674 ENSGACG00000017289 GI_35903182 997

ENSAMXG00000012474 ENSLOCG00000011537

5 SI


Figure S1 962 1000 947

Gene: fhl2

0.05 ENSPFOG00000022124 ENSPFOG00000003291 ENSXMAG00000002166 ENSORLG00000001848 ENSTRUG00000008468

1000

ENSTNIG00000017175

1000 877 GI_499025292

621

932 GI_548401457 941 GI_554818515

628

1000

GI_583995557 ENSONIG00000012307 ENSGACG00000015048

653 GI_548379261 429

771 GI_498986713 970 GI_554870366 1000 940


400 998

732

ENSTRUG00000013559 ENSTNIG00000000462 ENSPFOG00000015302

999

1000

ENSXMAG00000011596 ENSORLG00000012482

855 346 269

ENSAMXG00000009663 ENSDARG00000003991 ENSDARG00000042018 ENSAMXG00000005118 ENSLOCG00000008763

6 SI


Figure S1 0.1 GI_548356125 951

Gene: fkbp4

761

GI_498994696

997 GI_545786431

1000

GI_583988484

ENSONIG00000015051 747

ENSORLG00000008977

648

ENSPFOG00000018881

422 1000

ENSXMAG00000003963 1000 ENSGACG00000012979

ENSTRUG00000015044

ENSDARG00000008447 1000 ENSAMXG00000003846

ENSLOCG00000016880

7 SI


Figure S1 0.1 GI_498964459 474 GI_554815264

1000

Gene: flna 997 GI_548536083

1000

464

GI_584019220

ENSONIG00000017914

ENSGACG00000013098 456 ENSPFOG00000001616 1000 ENSXMAG00000004665 1000

414 ENSORLG00000001982

ENSTRUG00000003170 1000 ENSTNIG00000004951

ENSAMXG00000013411 1000 ENSDARG00000074201

ENSLOCG00000015505

SI


Figure S1 0.05 ENSTRUG00000000550 1000 ENSTNIG00000010510

459

Gene: gnb2l1

ENSGACG00000018103

GI_554821010 263 884

GI_498935526

998 569 GI_548334125

975

749

GI_583972285

ENSONIG00000012984

ENSORLG00000005276 891 ENSPFOG00000008165 998 ENSXMAG00000008940

601

ENSAMXG00000007457 603 ENSLOCG00000009758

ENSDARG00000041619

ENSAMXG00000002584

SI


Figure S1 0.1 GI_548419148 999 GI_499031622 860

Gene: grip1

940 GI_554820840

1000

GI_583971256

GI_542204218 409 ENSPFOG00000012379 1000 ENSXMAG00000006468 657 1000

ENSORLG00000017453

ENSTNIG00000002863 992 ENSTRUG00000005225 670 ENSGACG00000000177

ENSAMXG00000011215 798 ENSDARG00000015053

ENSLOCG00000016167

SI


Figure S1 0.1 GI_554823092 596 855 GI_499026510

Gene: kat5

531 GI_548385825

999

GI_584015024

ENSONIG00000005359 671 ENSTRUG00000016643 1000 ENSTNIG00000011743 538

809 ENSGACG00000020408

ENSORLG00000007458

ENSPFOG00000010293 1000 ENSXMAG00000005173

1000

ENSDARG00000045951 1000 ENSDARG00000004587

ENSAMXG00000009091

SI


Figure S1 0.05 ENSDARG00000005104 909 GI_597735797

ENSTRUG00000013732

Gene: limk2

1000

ENSTNIG00000015862

GI_554811068 994 928 GI_498956642

804

GI_548339212

1000 1000

849

GI_573905058

ENSONIG00000013399

ENSORLG00000006835

791

ENSPFOG00000009526

746

1000 ENSXMAG00000018076

ENSGACG00000008716

ENSLOCG00000004821

SI


Figure S1 0.05 ENSXMAG00000006444 1000 ENSPFOG00000006212

354

Gene: mapk1

ENSGACG00000014421

GI_554822617 240 GI_499004332

264

537

847 GI_548356923

1000

GI_584005676

ENSONIG00000014115

995 892

ENSTNIG00000015351 1000 ENSTRUG00000015300

SCAFFOLD5487_CONTIG129853

ENSAMXG00000001222 878 ENSDARG00000027552

ENSLOCG00000002024

3 SI



GI_554861523 544 336 885

GI_499019863

Gene: mapk3 1000 GI_548501870

276 1000

GI_584026649

ENSONIG00000019408 311 ENSORLG00000011993

ENSGACG00000013102

ENSTRUG00000005697 1000 1000

ENSTNIG00000011583

ENSAMXG00000017822

ENSDARG00000070573

4 SI


Figure S1 0.1 ENSAMXG00000015432 1000 ENSDARG00000075340

GI_554817925 539

1000

GI_499021221

1000 GI_548391342

1000

Gene: med1

GI_583992145

GI_542192331 637 ENSPFOG00000001519 1000 ENSXMAG00000002969 912 ENSORLG00000008300

1000

ENSTNIG00000004334 1000 ENSTRUG00000012065 997 ENSGACG00000006033

ENSLOCG00000012767

5 SI


Figure S1 0.1 ENSLOCG00000000694

ENSAMXG00000012890

ENSPFOG00000010829 1000 ENSXMAG00000008718 547 ENSTRUG00000014013 315

948 ENSTNIG00000003778

ENSGACG00000008017

GI_554866935 534 892 GI_584023652

Gene: med4

962 GI_548532252 994

685 GI_499031293

484 378

ENSONIG00000016177

ENSORLG00000014076

ENSDARG00000041503

6 SI



Gene: med12

GI_498964171 695

1000

544

GI_548340722

GI_554804436

1000 1000

ENSONIG00000002455

GI_584017139 838 ENSTNIG00000015746 1000 ENSTRUG00000012646 777

888 ENSGACG00000017493

ENSORLG00000000784

ENSAMXG00000011603 1000 ENSDARG00000056800

ENSLOCG00000015382

7 SI


Figure S1 0.1 ENSXMAG00000018016

1000

ENSPFOG00000009647

974

Gene: med13

ENSORLG00000005489 ENSTNIG00000003289

1000 1000

ENSTRUG00000007405

677

ENSGACG00000010389 970 774

GI_548404206

995 GI_499014114

1000

980 GI_554855577 GI_573890035

1000

ENSONIG00000011173 ENSDARG00000003910 1000

ENSAMXG00000002817 ENSPFOG00000024209

1000

ENSXMAG00000000108

747

ENSORLG00000012337 ENSGACG00000020213 1000

768 ENSTNIG00000009033 1000

ENSTRUG00000008851 972

565

GI_499021858

947 GI_548408649 996

975 GI_554832637 1000

GI_583987902 ENSONIG00000017544 ENSDARG00000053884

1000

ENSAMXG00000000953 ENSLOCG00000003727

SI


Figure S1 0.1 ENSTNIG00000014969 1000

Gene: med14

ENSTRUG00000013609

778

ENSGACG00000002015

ENSPFOG00000013987 1000 1000

ENSXMAG00000018007

962

ENSORLG00000010808

GI_554851281 520 824 1000

GI_499034639

999 GI_548378507

1000

GI_583985895

ENSONIG00000006848

ENSAMXG00000002581 1000 ENSDARG00000009953

ENSLOCG00000002286

SI



GI_499010815 648

1000

GI_554824751

1000 987

1000

GI_548370249

Gene: med16

GI_583990837

ENSONIG00000004564

ENSTNIG00000004736

693

1000 ENSTRUG00000007850

682

ENSGACG00000013385 792

ENSORLG00000000109

ENSAMXG00000018838 1000 ENSDARG00000040779

ENSLOCG00000001808

30 SI



ENSPFOG00000017880 1000 ENSXMAG00000007752

481

ENSORLG00000000709

GI_499047177 406 443

926

Gene: med17 GI_554887944

995 GI_548396051

1000

999 933

GI_584012931

ENSONIG00000001372

ENSGACG00000013203

ENSTNIG00000006440 1000 ENSTRUG00000004276

ENSLOCG00000007406

31 SI



GI_554858967 399

707

GI_548338012

1000 GI_499023404

Gene: med24

1000 1000

595

GI_584012330

ENSONIG00000019926

267

ENSORLG00000008227

ENSGACG00000008529 508 ENSTNIG00000012846 1000 ENSTRUG00000016382

ENSAMXG00000012180 1000 ENSDARG00000032459

ENSLOCG00000012864

32 SI



ENSTRUG00000003806 1000 ENSTNIG00000000448

GI_554852211 326

970

Gene: med30

GI_548477220

623 GI_498976995 892 991

ENSONIG00000013534

GI_583998619 358 ENSPFOG00000000737 1000 ENSXMAG00000014029 553

680 ENSORLG00000001732

ENSGACG00000003014

ENSLOCG00000003235

33 SI


Figure S1 0.1 GI_554840198 528

783

GI_498984261

Gene: ncoa1 998 GI_548530893

1000

GI_584022154

ENSONIG00000015724 956 ENSTRUG00000006619 1000 ENSTNIG00000019142 992 1000

ENSGACG00000006727

ENSPFOG00000004231 1000 ENSXMAG00000017782 736 SCAFFOLD1294_CONTIG113045

ENSDARG00000018257 1000 ENSAMXG00000010390

ENSLOCG00000015891

3 SI



1000

ENSXMAG00000001970

744

Gene: ncoa3

ENSORLG00000013704 925 GI_499042642

368

995 GI_548447463 1000 GI_554808986 1000

GI_583978807

1000

ENSONIG00000020313 ENSTRUG00000009516

1000 946

ENSTNIG00000007303 669 ENSGACG00000010036 ENSAMXG00000006902 999

ENSDARG00000077404 ENSAMXG00000008791

226

ENSAMXG00000008788 611 GI_548366017 991 GI_498965809 963 GI_554831335 1000

GI_584003095 ENSONIG00000017075

301

873 1000 649

ENSPFOG00000011587 ENSXMAG00000017470

961 ENSORLG00000012143

990

ENSGACG00000015221 ENSTRUG00000004450

524

1000

ENSTNIG00000012601 ENSAMXG00000008794 ENSLOCG00000003989

3 SI


Figure S1 0.1 GI_548457815 980

994

GI_499046546

Gene: ncoa4 995 GI_554883384

1000

GI_584024662

ENSONIG00000007129

614

ENSPFOG00000005630 505

1000 ENSXMAG00000002456

406 ENSORLG00000003269

ENSGACG00000012317

1000

ENSTRUG00000003924 1000 ENSTNIG00000013384

ENSDARG00000021439 804 ENSAMXG00000015735

ENSLOCG00000012898

3 SI


Figure S1 0.1 GI_498955057 635

772

Gene: nkx3.1

GI_554824085

995 GI_548354440

1000

GI_583977526

ENSONIG00000011762 599

SCAF14652 750

877 ENSGACG00000010776

1000

ENSORLG00000010925

ENSPFOG00000009654 998 ENSXMAG00000020262

ENSDARG00000078280 1000 ENSAMXG00000024837

ENSLOCG00000015015

3 SI


Figure S1 0.2 GI_554851579 965 GI_499021768 979

Gene: nrip1

982 GI_548408144

1000

GI_584025409

ENSONIG00000015866 637 ENSTRUG00000004236 1000 ENSTRUG00000000031 566 1000

ENSGACG00000020154

ENSPFOG00000017715 1000 ENSXMAG00000014033

1000 647

ENSORLG00000000586

ENSDARG00000068894 1000 ENSAMXG00000025737

ENSDARG00000068965 1000 ENSAMXG00000025365

ENSLOCG00000000906

3 SI


Figure S1 0.1 ENSTNIG00000003928

1000

ENSTNIG00000009549

1000 473

Gene: pias1

ENSTRUG00000016843 ENSGACG00000016894 898

GI_554840096

1000 GI_499013515 1000

1000 GI_548448896 1000

GI_583997712 ENSONIG00000013251

391

ENSPFOG00000006900

746 840

1000

ENSXMAG00000017552 ENSORLG00000002077 ENSDARG00000036094

1000

ENSAMXG00000006151 ENSPFOG00000009110

1000

ENSXMAG00000003583

574

330

ENSORLG00000006728 737

916

GI_498993905

854 GI_548355942 743 GI_554863406 808 1000

GI_583988189 ENSONIG00000015473

1000

ENSGACG00000005176 ENSTRUG00000015008 1000

ENSTNIG00000008434 ENSDARG00000062445

1000

ENSAMXG00000002784 ENSLOCG00000013933

3 SI


Figure S1 0.1 ENSPFOG00000000261 1000 SCAFFOLD_JH558015.1

GI_499015732 507 466 1000

GI_548377776

Gene: pias2

615 GI_554864979

301

1000

ENSONIG00000013927

GI_584015665

ENSORLG00000017353 1000 631 ENSGACG00000005099

ENSTRUG00000013569 1000 ENSTNIG00000003200

ENSDARG00000092979 1000 ENSAMXG00000002435

ENSLOCG00000006647

0 SI


Figure S1 0.1 ENSTRUG00000010930

1000

ENSTNIG00000018878

Gene: pik3r1

356 GI_554876860 907 GI_548541918 495 GI_499049716

1000

1000 536 449

GI_573878953 ENSONIG00000001749 ENSORLG00000017457

652 ENSPFOG00000015835 464 1000

ENSGACG00000001062

559 ENSGACG00000015820 1000 736

ENSPFOG00000001009 ENSXMAG00000018595

495 ENSORLG00000002670 ENSTRUG00000007584 1000 1000

ENSTNIG00000013464

GI_548334788 GI_554838849 992 GI_498981102 1000

GI_584003878 ENSONIG00000011065 ENSAMXG00000011959

1000

ENSDARG00000038524 ENSLOCG00000010510

1 SI

ENSXMAG00000015104


Figure S1 0.1 309 ENSPFOG00000024225 1000 ENSPFOG00000023056 1000

ENSPFOG00000000170

976

ENSXMAG00000002484

Gene: pik3r2

LOC101163728 739 GI_499028291

1000

914 GI_548356312 970 GI_554849340 992 GI_583993919

1000

ENSONIG00000012700 1000 ENSGACG00000008201 ENSTRUG00000007054 1000

ENSTNIG00000010197

423 GI_498942969 994 GI_554819907 422

1000 GI_548336831 1000

GI_583983019 ENSONIG00000010477

996

ENSPFOG00000003942 920

1000

ENSXMAG00000013889 ENSGACG00000015520

1000

ENSTRUG00000010476 935

ENSTNIG00000011070 ENSDARG00000018060

553

XM_007236673.1 ENSLOCG00000001519

2 SI


Figure S1 0.05 GI_494461325 446

GI_545793510

Gene: pmepa1

830

999 GI_545786152

1000

814

GI_573906092

ENSONIG00000004438

ENSORLG00000012800 657

ENSXMAG00000010456

1000 ENSPFOG00000001516

1000

ENSGACG00000003728

ENSAMXG00000013100

ENSDARG00000039325

3 SI


Figure S1 0.05 GI_498980257 658

Gene: ppap2a GI_548335165 923

865

1000

GI_554813089

GI_583987884

ENSONIG00000007599 529

ENSPFOG00000003517

1000 ENSXMAG00000004780

ENSORLG00000005464

1000

ENSDARG00000053381

ENSAMXG00000018732

SI


Figure S1 0.05 GI_548425231 620 GI_498999424 951

Gene: ppargc1a

996 GI_554850044

1000

GI_584018961

ENSONIG00000007635 1000 ENSPFOG00000001263 1000 ENSXMAG00000007748 1000

505

ENSORLG00000004788

ENSTRUG00000007210

1000 1000

ENSTNIG00000002174

ENSGACG00000019546

ENSAMXG00000002461 1000 ENSDARG00000067829

ENSLOCG00000012350

SI



1000

ENSXMAG00000014454 645

ENSGACG00000009998 ENSTNIG00000005984

1000

GI_548428164 466 822 GI_499029140 806 GI_554877417 928

586

1000

GI_583996646 ENSONIG00000019123 ENSORLG00000020711

ENSDARG00000071018 971

ENSAMXG00000010994 727

GI_548350440

975 GI_498987823 1000

994 GI_554806495 1000 398


217

ENSTRUG00000009851 523 1000

ENSTNIG00000013318 ENSPFOG00000015747

980

1000

ENSXMAG00000012957

ENSORLG00000006231 ENSAMXG00000007753 908

ENSDARG00000056623 ENSLOCG00000006145

SI


Gene: pten

Figure S1 0.1 ENSTNIG00000009166

1000

ENSTNIG00000009167

1000

Gene: ptk2a

ENSTRUG00000007362

522

ENSGACG00000004003 1000

ENSGACG00000004011 GI_498978332 769 847 GI_548352657

433

737 GI_554813630 451

GI_583985834

1000

ENSONIG00000002815 994

ENSXMAG00000015476 1000

ENSPFOG00000003397 SCAFFOLD5001_CONTIG128876 ENSTRUG00000011167

1000

ENSTNIG00000009636

998

ENSGACG00000007004

1000 880

833

GI_548435043

941 GI_554849438 856 GI_499029030 504

GI_573896657

993

688

ENSONIG00000006838 ENSXMAG00000010911

1000 1000

ENSPFOG00000010090 ENSORLG00000004751 ENSDARG00000040197

972

ENSAMXG00000004491 ENSAMXG00000018637

1000

ENSDARG00000004672 ENSLOCG00000007702

SI


Figure S1 0.1 726 GI_554877844 998 GI_499049776 990 GI_545793246

Gene: ptk2b

1000

GI_584025201

534

ENSONIG00000015175 ENSGACG00000014838

830 1000

ENSPFOG00000009145 ENSXMAG00000004406

1000

777 ENSORLG00000005884 ENSTRUG00000017337

523

1000

ENSTNIG00000014508

ENSAMXG00000000798 996

ENSDARG00000022841 833

GI_498939798

967 GI_548381009 999 GI_554807097 1000

GI_584004629 ENSONIG00000015297

424

ENSXMAG00000004048 629

1000

ENSPFOG00000008438 ENSTRUG00000008406

1000 1000

ENSTNIG00000016347 952 ENSGACG00000010609

1000

ENSORLG00000008993 ENSAMXG00000019303 1000

ENSDARG00000039577 ENSLOCG00000017241

SI



1000 476

ENSXMAG00000011081 ENSXMAG00000011307

794 425

ENSPFOG00000015319 ENSXMAG00000011073

1000

ENSPFOG00000015350

523 997

557

ENSXMAG00000011324 ENSORLG00000003527

ENSGACG00000009531 9 8 GI_548338137 2 GI_499023276 8 GI_554845115

488

966

GI_584012219

1000

ENSONIG00000019847 ENSTRUG00000016765 996

Gene: rac1

ENSTNIG00000012875 GI_499014998

52

8 GI_548382828 GI_554829718 88 7 9 GI_583992732 ENSONIG00000017151

779

5 88

926

894 GI_499014994

478

GI_583992724 ENSONIG00000017149

1000 757

ENSGACG00000011601 996 ENSXMAG00000001114 ENSPFOG00000004946

403

1000

GI_548382840 GI_554829712

1000 1000

ENSORLG00000008757 ENSORLG00000008763

ENSTRUG00000016201 ENSTNIG00000017983 950

ENSDARG00000096666 ENSDARG00000013203

1000 869 994

ENSDARG00000096549

999

ENSDARG00000054649

ENSDARG00000074849 ENSAMXG00000008935

687 1000

ENSDARG00000087954 ENSDARG00000099506

ENSLOCG00000008397 SI



Gene: raf1 GI_548483383 723 941

896

GI_554857802

714

1000

1000

GI_498965606

GI_584003028

ENSONIG00000017170

655

ENSORLG00000011471

ENSTNIG00000012621 1000 743

ENSTRUG00000006611 787 ENSGACG00000000060

ENSDARG00000096415 992 ENSAMXG00000001055

ENSAMXG00000005440

ENSLOCG00000013974

0 SI


Figure S1 0.1 GI_583972026

699 GI_498962091

Gene: ran

321 GI_554805068 665 488 GI_548341336

ENSPFOG00000009552 991 ENSXMAG00000009922

689 915

ENSORLG00000003452

ENSONIG00000005139

996

ENSTRUG00000013749 998 ENSTNIG00000013137 661 ENSGACG00000017755

ENSDARG00000057026 907 ENSAMXG00000015390

ENSLOCG00000008279

1 SI


Figure S1 0.1 GI_548387323 643

Gene: rb1

936

GI_499026357

997 GI_554822936

1000

GI_584014918


984 ENSORLG00000008317

1000

ENSGACG00000020379

ENSTRUG00000015842 1000 ENSTNIG00000011786

ENSDARG00000006782 1000 ENSAMXG00000005363

ENSLOCG00000008882

2 SI



GI_548443896 399 797

Gene: rhoaa

609 GI_584019304 841 GI_554866988

1000

GI_498964222 ENSONIG00000017974

GI_554807569 503

42 GI_583980905 730 GI_499016231 1000

290 GI_548370620

570

ENSONIG00000012367

ENSGACG00000009938 1000 ENSTNIG00000015015 836 ENSTRUG00000010405

ENSDARG00000015429 569 ENSDARG00000026845 351 ENSAMXG00000014632

ENSLOCG00000014301

3 SI


Figure S1 0.1 ENSDARG00000094673

915 ENSAMXG00000005847 286

GI_554862978

268 GI_498957597

Gene: rhoab

995 GI_548414713 985 536

GI_583976140 ENSONIG00000018884

783

ENSPFOG00000019065 681

999

ENSXMAG00000016892

566 ENSGACG00000001206 987

ENSORLG00000018734 ENSTNIG00000014672 918

738

ENSTRUG00000011944 ENSAMXG00000008373

ENSPFOG00000000160

999

ENSXMAG00000019368 387

568

GI_548357349

796 GI_498997689 900 GI_554857836 553 999

GI_583980256 ENSONIG00000001670

649

ENSGACG00000005670 ENSTNIG00000006051 949

ENSTRUG00000010942 ENSLOCG00000014438

SI



Gene: rhob

GI_499036281 582

596

GI_548358324

576 GI_554821869 1000

1000

GI_583994917

515

ENSONIG00000020448

553

ENSORLG00000012619

ENSGACG00000009667 665 ENSTRUG00000018178 875 ENSTNIG00000002278

ENSAMXG00000026330

ENSLOCG00000017876

SI


Figure S1 0.1 ENSTRUG00000017344 1000

Gene: rnf4

SCAF7445

752

ENSGACG00000016217 437 ENSPFOG00000017123 1000 ENSXMAG00000015165 969 ENSORLG00000020573

1000

GI_554877732 794

851

GI_548333174

512 GI_499025880

999

GI_542256685

GI_583973152

ENSDARG00000090993 951 ENSAMXG00000007606

ENSLOCG00000006957

SI


Figure S1

1000

0.2 ENSXMAG00000002519 ENSPFOG00000019210

977

ENSORLG00000011566

501

ENSTRUG00000004900 1000

1000

ENSTNIG00000006782 ENSGACG00000006180

GI_498982921

953

954 GI_548351054

Gene: rnf14

742 GI_545785817 457

1000 GI_583979411 ENSONIG00000008460 880 1000

ENSPFOG00000006823 ENSXMAG00000001585

880 784 ENSORLG00000001462 ENSTNIG00000018203 986

1000

ENSTRUG00000008815

ENSGACG00000020731

959

ENSDARG00000090710 ENSDARG00000078683

999

ENSDARG00000091727 974

972

963

ENSDARG00000002794

ENSDARG00000043905 ENSAMXG00000020091 ENSLOCG00000010578

SI


Figure S1 0.05 ENSDARG00000058993 999 ENSAMXG00000014672

ENSPFOG00000011127 1000 ENSXMAG00000002398

GI_498945850 875 862 1000

GI_548422536

1000 GI_554803283

826 1000

GI_583994033

GI_542206027 759 ENSORLG00000017642

ENSTRUG00000013281 1000

1000 ENSTNIG00000008471

ENSGACG00000017327

ENSLOCG00000001989

SI


Gene: rock1


1000

ENSXMAG00000013653

441

ENSORLG00000012731

Gene: rock2 GI_548358264

882

932

1000 GI_499036295 1000 GI_554821891 484

GI_583995367

1000

GI_542255251 1000 ENSGACG00000009555 ENSTRUG00000018218

1000

1000

ENSTNIG00000012308 ENSAMXG00000003869

1000

ENSDARG00000004877 958

GI_499017063

999 GI_548401842 986 GI_545786390 1000

GI_584008970 GI_542208870

472

1000 1000

1000

586

ENSPFOG00000012199 ENSPFOG00000012091 ENSXMAG00000009185 ENSORLG00000018255

1000

ENSTRUG00000010769 ENSTNIG00000008912

980

934 ENSGACG00000012788 ENSAMXG00000021207 1000

ENSDARG00000017500 ENSLOCG00000016666

SI



1000

ENSXMAG00000001476

Gene: src

514

780

GI_548412532

933 GI_499019153 506 GI_554816133 GI_583997963

1000

522

ENSONIG00000016547 ENSTRUG00000005980

1000

1000

ENSTNIG00000019527 427 ENSGACG00000011349 971 ENSORLG00000016183 ENSAMXG00000001275 914

ENSDARG00000008107 581

GI_554866558

593 GI_548355415 903 GI_498971516 1000

GI_583974949 ENSONIG00000006882

423

ENSPFOG00000013135 547

1000

863

1000

950

ENSXMAG00000010238 ENSORLG00000006714 ENSTRUG00000018366

1000

ENSTNIG00000018270 ENSGACG00000005548 ENSAMXG00000014517

ENSLOCG00000002309

0 SI


Figure S1 0.1 SCAFFOLD_JH591692.1

ENSAMXG00000020290

ENSPFOG00000007368 963

Gene: tgfb1i1

ENSXMAG00000018458

GI_548490449 797 746 999

GI_499048970

945 GI_554875222

588 998

GI_584022201

ENSONIG00000011521 254 ENSORLG00000005775

ENSTRUG00000005520 572

963 ENSTNIG00000018936

ENSGACG00000007235

1 SI


Figure S1 0.1 ENSDARG00000044459

1000

ENSDARG00000040095

1000

ENSAMXG00000001863 ENSTNIG00000012194

1000 1000

ENSTRUG00000010702

1000

ENSGACG00000013745 ENSPFOG00000013297

1000

ENSXMAG00000014797

941

1000

ENSORLG00000014550 783 1000

GI_49898548

1000 GI_548389984 999 GI_554830071

Gene: thrap3a

GI_583993177

1000

GI_542234433 955

GI_548406882

960 GI_554857382 955 GI_498976772 1000

GI_583998686 ENSONIG00000013673

979

ENSGACG00000002319 530 1000

ENSTNIG00000004582 1000

1000

ENSTRUG00000010336 ENSPFOG00000000525 ENSXMAG00000017962

1000

975 ENSORLG00000009543 ENSAMXG00000020877 1000

ENSDARG00000003513 ENSLOCG00000002939

2 SI


Figure S1 0.1 GI_548467978 543

612

GI_554857247

Gene: ube3a 533 GI_499026835

1000

GI_584015939


749 ENSORLG00000020667

ENSTRUG00000006347

1000 1000

ENSTNIG00000014475

ENSGACG00000015321

ENSDARG00000055737 1000 ENSAMXG00000012931

ENSLOCG00000008388

3 SI


Figure S2 Site-wise Ka/Ks estimates using Selecton under the M8 model allowing for positive selection. In case positive selected sites were detected, they were compared to the null model M8a. If the likelihood ratio test returned significant results for positive selection, these are indicated below the sequence.

SI


Figure S2

Gene: akt1

1 MNEVVIVKEG 51 PLNNFSVAQC 101 KTIQAVADSL 151 EYLKLLGKGT 201 VLQSSKHPFL 251 RFYGAEIVSA 301 KDGATMKTFC 351 NQDHEKLFEL 401 EVMQHKFFAG 451 PPGQDDNMES

11 WLHKRGEYIK 61 QLMKTERPKP 111 QKQEEEMMDC 161 FGKVILVKEK 211 TGLKYSFQTH 261 LDYLHSEKNV 311 GTPEYLAPEV 361 ILMEDIRFPR 411 IVWQDVYEKK 461 MDSERRPHFP

21 TWRPRYFLLK 71 NTFIIRCLQW 121 RSGSPSDNIG 171 ATGRYYAMKI 221 DRLCFVMEYA 271 VYRDLKLENL 321 LEDNDYGRAV 371 TLAPEGQSLL 421 LIPPFKPQVT 471 QFSYSASGTA

31 SDGTFIGYKE 81 TTVIERTFHV 131 IEDMEVYLTK 181 LKKEVIVAKD 231 NGGELFFHLS 281 MLDKDGHIKI 331 DWWGLGVVMY 381 SGLLKKDPKQ 431 SETDTRYFDE

Legend: The selection scale:

1

2

3

4

Positive selection

SI

5

6

7

Purifying selection


41 RPQDVDQLET 91 ETPEEREEWT 141 PRLKVTMHDF 191 EVAHTLTENR 241 RERVFSEERA 291 TDFGLCKEGI 341 EMMCGRLPFY 391 RLGGGPDDAK 441 EFTAQTITIT

Figure S2

Gene: ar 1 MRQTNRQLPH 51 LGSRSEFSSV 101 GDALVESSNS 151 SLVSDRSQEN 201 MLKRVHANTT 251 MDGGHTVFCQ 301 EENSEEVAAY 351 THPQNTGQGT 401 GDWMEVPYTD 451 GSCKVFFKRA 501 GARKLKKIGQ 551 EPEVVNAGHD 601 DDQMTVIQHA 651 YDHCIRMKRL 701 RTNYIHELDR 751 FVQAQSYPTK

11 RGLCIGTSHI 61 TKADDVEEGA 111 DIASTTISET 161 YLFQMHLADR 211 PEVVPSQHIS 261 FDQSVRPNPA 311 PPEYRVRIKK 361 GSSFACNAYG 411 IRFESGRENL 461 AEGKQKYLCA 511 LKGLEEAGNQ 561 NAQPDSAACL 611 WMGVMVFALG 661 AQEFAWLQIT 711 LVSSGRKTSS 761 VNFPEMMSEI

21 SDTGVKEVQS 71 YGFLPGLQGN 121 ARELCKAVSV 171 SANGTGVTVT 221 AAHSKQDGHE 271 AYGQNDPLSV 321 EVSNEHADVW 371 EDGVSPEQWY 421 FPMEYFFPPQ 471 SRNDCTIDKL 521 NPIETVQCMS 571 LTSLNELGER 621 WRSYKNVNAR 671 QEEYLCMKAL 721 NYSQRFFQLT 771 ISVQVPKMLA

31 ISFPRQTDVL 81 TEQKSSIPIP 131 SLGLNMDPNE 181 DYKCPIANDG 231 SRLNAELSNA 281 EQGNVASHGL 331 PVQYRYSDNG 381 SGGMVGRVPY 431 RTCLICGDEA 481 RRKNCPSCRL 531 PKPSITTHTQ 581 QLVKVVKWAK 631 MLYFAPDLVF 681 LLFSIIPVEG 731 QLMDSLQPIV 781 GMVKPILFHK


1

2

3

4

Positive selection

SI

5

6

7

Purifying selection


41 ARSSHFAKRL 91 PHHRKETKTH 141 MNDLGTSHDP 191 PSVQSHENIR 241 TCEDSENHMN 291 YKCEAFPNAS 341 NTPYGLIRQF 391 TSSSCLKNEM 441 SGCHYGALTC 491 RKCFEAGMTL 541 PVFLNILESI 591 GLPGFRSLHV 641 NDHRMHISSM 691 LKSQTYFDEL 741 RMLHQFTFEL

Figure S2

Gene: arid1a

1 MAAQVASVAT 51 QKELQDGADG 101 MAHHHPAAFP 151 DSYQPNSHDH 201 PAKQQQQQPP 251 TRGYQNYPPS 301 STGQPLSRNQ 351 PGQGYGPPTP 401 ASYYSQQAQP 451 PHQTPQSQAQ 501 PPPPQQQQQP 551 QQQQQPSPYQ 601 GRPSSLPDLS 651 HTSPHLPGIR 701 ESILHPSMNQ 751 GMGPYQQNNS 801 PMPGQGGGPP 851 PPGGLNRKAQ 901 NSMPGMMNPQ 951 DGTPKPETKS 1001 SI

11 LNTSPPSELK 61 GNAGGGGDPE 111 PPPYGYSPHY 161 GFPNHQFNNY 211 PPAGGTTAMA 261 DYSNQEGANK 311 PSSPMDQMGK 361 QRYPMGMQSR 411 PHAAQQQSPY 461 QQQQQQQQQP 511 PSQPPPPQPT 561 RFPPPPQELS 611 GSIDDLPTGT 661 GPSPSPVGSP 711 SAMGQDRVYM 761 MGNYGPQGAQ 811 YTGMPPGRMG 861 EAAAAAMHAA 911 GPPYPMGGNM 961 KKSSSSTTTN 1011

21 KADRDPQEEP 71 MKNGNGNPSR 121 GRGPFHQHGG 171 SPFPNRTAYP 221 VTYNNQRYTM 271 GPVDVGSSSQ 321 MRGQPYAAAN 371 TPGGMGSMQY 421 PQQPQSQPGA 471 PPVPPQSQAP 521 PATQPQSQQP 571 QDSFSSQSSV 621 EGALSPGVST 671 ASVTQSRSGP 721 QRNPQMPAYG 771 YGPQGYPRQP 821 PGQMGTRPYG 871 VNSSHNRPPG 921 PNNTAGMAPS 971 EKITKLYELG 1021

31 VPGEKQQENK 81 VNNNNNQNDS 131 QQSPGMAAAA 181 GQGYTMNSPR 231 GNPQPTSTPT 281 YGGHQGWQQR 331 PYSQQPQQGP 381 GQQMPPYGQQ 431 QTPYSQPSAP 481 YSQSQAPQSA 531 PGHAPPQQSQ 581 PPSNPAMASS 631 SGVSSSQGEQ 681 LSPAGVPGTQ 731 SPQPGSALSP 781 NYTGMPNASY 831 PNMGPNMGSM 881 YPNMPQSGMI 931 PELMGLDVKL 981 PEPERKMWVD 1031


41 EPGSESGSPG 91 GAPEGNNHPG 141 GPAVQPGSMM 191 NNQPPAAGGQ 241 LNQLLTSPSS 291 THHPPPMSPG 341 PPGSQQGASY 391 GPAGYGQQGQ 441 LAQAQPPYSQ 491 QPPYPQQQVP 541 AAPYSQAPPQ 591 KSGSEDVNMQ 641 SNPAQSPFSP 691 MPPRPPSGQS 741 RQSSGGQMHA 791 PGPGMGGSMN 841 PPQVGSGMCP 891 PAGTPYGQSM 941 NQAQKMNNKA 991 RYLAFTEEKA 1041

Figure S2 MGMNNLPAVG RKPLDLFRLY VSVKEIGGLT QVNKNKKWRE LATNLNVGTS

1051 SSAASSLKKQ 1101 AGSGSLQGPQ 1151 LQDPFADSSD 1201 RKGGEFMSPG 1251 EPGMGPEGSM 1301 QGAPSGGPYP 1351 QQQQQAQQQT 1401 ATAGPNSQQS 1451 AAQGPGYHSM 1501 RPLQPNYQTP 1551 GPPVPASHIT 1601 PEAWRVMMSL 1651 VEYFRRCLIE 1701 EAEEMEEEDE 1751 QQEEQEGEAA 1801 VVDCSDKLGR 1851 PASGGSAGRK 1901 SMTVEAVRGT 1951 IADWQDSLAK 2001 EHPERKQAPL 2051 QLDLSIYPES 2101 ETLSKLSIQD 2151 SI

1061 YIQCLYAFEC 1111 TPQSTSSSMA 1161 PAFPRRNSMT 1211 QGPNSGMGEQ 1261 GPGAPQPNLM 1311 NQPPGMYAQQ 1361 APPAQQEMYS 1411 MPPQMMGSPM 1461 NRSEEMMPSD 1511 PAIQNHIPQV 1561 PAPVQPPLIR 1611 KSGLLAESTW 1661 IFGILKEYEV 1711 DEDEEQPEAS 1761 VKDPSVLTLS 1811 LQEFDSGLLH 1861 KSPAGENVTE 1911 PESHKENSKF 1961 RCICVSNIVR 2011 TYEKEEEEDE 2061 ICLPLLDGLL 2111 NNVDLILATP 2161

1071 KIERGEDPPP 1121 EGGDLKPPTP 1171 PNSAYQQGMN 1221 YNRAPPGSMG 1271 PSNADTGMYS 1321 QPNYKRPVDG 1371 QYGNAYAGSE 1421 QSTPDGPQGS 1471 QRMNHEGQWP 1521 SSPAPMPRPI 1571 RDITFPPGSI 1621 ALDTINILLY 1671 GDPGQRTLLD 1721 EQQQQQQQTP 1771 QDTGTAQEKP 1821 WRIGGGDTTE 1871 GVEKVKTSEE 1921 LFSINPAQSH 1971 SLSFVPGNDL 2021 GVSCEKDEWW 2071 HWAVCPSAEA 2121 PFSRLEKLYG 2171

1081 DIFSAAEAKK 1131 ASTPHSQMPP 1181 TPDMMGRMPY 1231 NMGMGQRQQY 1281 PSRYPPQQQR 1331 GYGPPAKRHE 1381 RRPPGPQNQF 1431 MWPNRNDMGY 1481 AHVNQRQPPY 1531 ESRTSPSKPF 1581 EATQPILKPR 1631 DDNSIATFSL 1681 PEGLNSERDT 1731 QPPALEKQEG 1781 KQASKFDKLP 1831 HIQTHFESKL 1881 QPPAKSITAT 1931 RNIKILEDEP 1981 EMSKHPGLLL 2031 WDCLELLREN 2081 QDPFPTLGVN 2131 TLVRLVGERK 2181


1091 NQPKIQPPSP 1141 MPGVRSSVVS 1191 EPNKDPFSAM 1241 PYGPGYDRRQ 1291 HDSYGNQYPG 1341 GEMYNVPFSG 1391 PFQFGRERVQ 1441 NFPNRQGPGA 1491 GPSGPVPPMT 1541 MHSGIKMQKA 1591 RRLTMKDIGT 1641 CQLPGFLELL 1691 GSEDEEQEPE 1741 EQQNGERAGE 1791 IKLVRKKDPF 1841 DLLQARKRVP 1891 IDDVLSARPG 1941 RSKDETPLST 1991 LLGRLILLHH 2041 TLVTLANISG 2091 GVLSPQRLVL 2141 IPVCREMAVV 2191

Figure S2

LLANLAQGDS 2201 SAPFEPTSVD 2251 LVSHVICDVL

LAARAIAVQK GSIGNLLGFL EDSLAATQFQ QSQSSLLHMQ 2211 2221 2231 2241 MMRRAARALH AMAKVEENHS EFTLYESRLL DISVSPLMNS 2261 FLIGQS


1

2

3

4

Positive selection

SI

5

6

7

Purifying selection


Figure S2

Gene: brca1 1 MAAPTCKVED 51 HLSGSKRAGA 101 KYFSEVLLEQ 151 EAAISSAAAA 201 VTDPVIPVRL 251 KVSSNKILEK 301 ATEKCDELVQ 351 DRKGSSKEHQ 401 GGRVRSESLH 451 QPDRQERKGK 501 ADSAGPWKPT 551 RCTGRRLRTE 601 TEVLKVSEGY 651 SALDISEGPD 701 SFNLLPSPEY 751 ETENSGCTDI 801 RDRNGRRKKT 851 NRQIPIDGLP 901 STGPNISQES 951 NPRKRMRARM 1001 0 SI

11 VKQVVSMIRR 61 QCPLCKAEVT 111 KNGLGGLTEA 161 KEGFAKLMDL 211 HMGNNRDLTS 261 RRKTSVQKVM 311 ECVESLKKTD 361 ANKKVCKRKS 411 VLVSDGNQPE 461 KSKPNTKDNR 511 INETEAQIES 561 DSELERDPQA 611 EDIQQQSGHI 661 TGSDVAVMDE 711 PSQESEFCDN 761 IPPTKPASPS 811 KMDESTLGSV 861 QENESLVENC 911 SMTPDGLLPL 961 LESSDSDSNT 1011

21 NLECPICLDL 71 KRSLQDSSRF 121 QAIGTKTRAE 171 DDSSYFANSG 221 SREEEEHSFV 271 DWLSRIDEKA 321 RRSTLEDQVF 371 NELTPADFIK 421 IEQRPSPSQR 471 KRNALTRKKA 521 YPSSEEPAGR 571 PDQSENDQAG 621 VVESSLVSII 671 LLPGELTEGK 721 KASEKNENPE 771 CRNVDIKSAD 821 RGRKKNLNLS 871 KVKSTMKESF 921 RAVASDRADN 971 EEDLPSLAEL 1021

31 LRDPVSTRCD 81 KQLVEALQRT 131 SSACERLGGR 181 TAVAGSSEPT 231 SASKGENKTF 281 CFPEEENRPA 331 GVVYKRARRT 381 RPSPVAETSD 431 TARAETTQAG 481 IKAAKPLDLV 531 AGEPHATRRS 581 MLTCKGVEQL 631 RNAESPCNSN 681 NDSELETEQI 731 EEKGQVNVAV 781 KISDGSTSTF 831 SIHFSQVPPN 881 VGNGEQSDFV 931 EEQCLPGEGK 981 LGPKQPATNP 1031


41 HQFCRMCMLK 91 IHAFEQDTGT 141 ITDSESQQEL 191 TQDRERSAAD 241 DVSEKSKTNN 291 ETPSDADSLL 341 SAQLNKSFSS 391 ATSQPARSDA 441 GSWKDEEEDL 491 SCQQNNTGQD 541 RRLQLLTEKV 591 CESSEKENET 641 KAFKGDQLVP 691 LKTFKISKRR 741 ERTSLQSEHV 791 SSICTDSQRP 841 TEQLVCASLL 891 QSFPLARKEL 941 EQLSQWSLNS 991 QEDSNQWNPL 1041

Figure S2

QNRDLEASPS 1051 LVETESSQSE 1101 TVVAQQSTET 1151 GKHIFYPGFS 1201 RVSADRGAAR 1251 IMKTDPELVC 1301 GDVINGRNHQ 1351 CGATVAKEPF 1401 WVLDSVALYS

STVESSVVLP 1061 ILTTQQKDTI 1111 QPVSHEFRAL 1161 VFILSSCFEG 1211 GRMVLVGSGL 1261 ERTLKYFLGI 1311 GPRRARTATR 1361 LFTYNPELIQ 1411 CQALDSYLVK

VQQSVPASQG 1071 QKDLRRIEEE 1121 PCHVQLNKSV 1171 LLSVAKLGIG 1221 DRSELIMVQK 1271 AGRMWVVSFL 1321 EELLLSNYEI 1371 VVVVQPEAEE 1421 PLS

SVDLFSTQSD 1081 MAVLEAALKG 1131 KRNLIKPLEK 1181 TTKQSGSSGA 1231 FARKMDGTLA 1281 WIRECFRQGQ 1331 CCHGSFTDMT 1381 SQTDYKALQR


1

2

3

4

Positive selection

1 SI

5

6

7

Purifying selection


SPSHRIEQID 1091 QPDYPKSSLQ 1141 HANENTNIKP 1191 CDASGPIPNP 1241 AQVTPGTTHV 1291 LLDEAAFEVK 1341 TGQLEWMVEL 1391 KYSARVVTRE

Figure S2

Gene: cav1 1 MTGGIKDEES 51 IDLVNRDPKH 101 CYRLLTALVG 151 SICIHTFCDP

11 EGFLHSPFIR 61 LNDDVVKVDF 111 IPLALIWGLF 161 LFEAMGKVFS

21 KQGNIYKPNN 71 EDVIAEPEGT 121 FAILSFLHIW 171 GVRVSMTKEV

31 KSMDNDSMNE 81 HSFDGIWKAS 131 AVVPCVKSYL


1

2

3

4

Positive selection

2 SI

5

6

7

Purifying selection


41 KAMHDVHTKE 91 FTTFTVTKYW 141 IEIQCVSRVY

Figure S2

Gene: ccne1 1 MPRKNLKTGL 51 KKQYDTQTSW 101 ITPTRSSPLP 151 ILLDWLMEVC 201 FIAAKLEEIY 251 MSWLNIYMQV 301 GVLAASALFH 351 KKFKGIAADD 401 PPSSEKTGVS

11 QTEANDEVTK 61 NPATGCTSPC 111 VLCWANKDDV 161 EVYKLHRETF 211 PPKLHQFAYV 261 AYLKESSEML 311 FSSVELVQKV 361 LHNIQTHAAL 411 ES

21 ERSTTRSRKR 71 RLICTPDKEV 121 WNNLLQKDKV 171 YLAQDFFDRF 221 TDGACTEDEI 271 IPQYPQTTFV 321 SGYQLQDLEP 371 LEWLEKAYAY

31 KADVAIHLQD 81 DEPVALNDVG 131 YVRDNRFMER 181 MATQMNVVKT 231 LDMELIIMKE 281 QIAELLDLCA 331 CVKWMVPFAM 381 EAMGLDQNQR


1

2

3

4

Positive selection

3 SI

5

6

7

Purifying selection


41 PDEEVIEMTN 91 CAQYMFKNIF 141 HPHLQPKMRA 191 RLQLIGISSL 241 LKWSLSPLTA 291 LDVRCLEFSY 341 SIREVGSSEL 391 SPVPLSVLTP

Figure S2

Gene: cdc42 1 MQTIKCVVVG 51 YTLGLFDTAG 101 ITHHCPKTPF 151 AVKYVECSAL

11 DGAVGKTCLL 61 QEDYDRLRPL 111 LLVGTQIDLR 161 TQKGLKNVFD

21 ISYTTNKFPS 71 SYPQTDVFLV 121 DDPSTIEKLA 171 EAILAALEPP

31 EYVPTVFDNY 81 CFSVVSPSSF 131 KNKQKPITPE 181 EPKKKRKCKL


1

2

3

4

Positive selection

SI

5

6

7

Purifying selection


41 AVTVMIGGEP 91 ENVKEKWVPE 141 TAEKLARDLK L

Figure S2

Gene: cdk7 1 MAVDVKSRAK 51 AKDGINRTAL 101 IIKDTSLVLT 151 LKLADFGLAK 201 CILAELLLRV 251 MFPGTPLEHI 301 PTPGPQLPRP

11 RYEKLDFLGE 61 REIKLLQELS 111 PANIKAYILM 161 AFGSPNRVYT 211 PFLPGDSDLD 261 FSAAGDDLLD 311 NCSVEALKEQ

21 GQFATVYKAR 71 HPNIIGLLDA 121 TLQGLEYMHQ 171 HQVVTRWYRS 221 QLTKIFEALG 271 LLRGLFTYNP 321 ENFKIGVKRK

31 DKNTNTIVAI 81 FGHKSNISLV 131 HWILHRDLKP 181 PELLFGARMY 231 TPTEETWPGL 281 CTRITATQAL 331 RDGTEQGSLK


1

2

3

4

Positive selection

SI

5

6

7

Purifying selection


41 KKIKVGHRAE 91 FDYMETDLEV 141 NNLLLDENGV 191 GVGVDMWAVG 241 TSLPDYISFK 291 KKRYFSNRPG 341 KKLIF

Figure S2

Gene: cfl1l 1 MASGVAVHDD 51 SELHVRDLQP 101 WAPENAPLKR 151 GGKGLVVSVE

11 VVNIFNAMKV 61 GEDIFKRVVG 111 KMIYASSKNA 161 GKPI

21 RKAGEAEQDR 71 LLPEKDCRYA 121 LRSKLTGIKF

31 LKAILFRLSN 81 LYDSSYETKD 131 EWQINEMGEI


1

2

3

4

Positive selection

SI

5

6

7

Purifying selection


41 DEKQIIVDEG 91 SKKEDLVFIM 141 KDPSTLVEKF

Figure S2

Gene: ctnnb1 1 MATQADLMEL 51 NPEDDDVDNQ 101 TLDEGMQIPS 151 AIPELTKLLN 201 MQNTNDVETA 251 LFYAITTLHN 301 QILAYGNQES 351 SNKPAIVEAG 401 LGTLVQLLGS 451 LRAGDREDIT 501 SHWPLIKATV 551 SMGGTQQQFV 601 LLYSPIENIQ 651 ATYAAAVLFR 701 AQGEPLGYRQ 751 GLPDLGHAQD

11 DMAMEPDRKA 61 VLYEWETGFS 111 TQFDGAHPTN 161 DEDQVVVNKA 211 RCTAGTLHNL 261 LLLHQEGAKM 311 KLIILASGGP 361 GMQALGLHLT 411 DDINVVTCAA 461 EPAICALRHL 511 GLIRNLALCP 561 EGVRMEEIVE 611 RVAAGVLCEL 661 MSEDKPQDYK 711 DDPSYRSFHS 761 LIEGLPPGDS

21 AVSHWQQQSY 71 QSFTQDQVAD 121 VQRLAEPSQM 171 AVMVHQLSKK 221 SHHREGLLAI 271 AVRLAGGLQK 321 QALVNIMRTY 371 DPSQRLVQNC 421 GILSNLTCNN 471 TSRHQDAEMA 521 ANHAPLREQG 571 GCTGALHILA 621 AQDKEAAEAI 671 KRLSVELTSS 721 GGYGQDAMGM 771 NQLAWFDTDL

31 LDSGIHSGAT 81 IDGQYAMTRA 131 LKHAVVNLIN 181 EASRHAIMRS 231 FKSGGIPALV 281 MVALLNKTNV 331 TYEKLLWTTS 381 LWTLRNLSDA 431 YKNKMMVCQV 481 QNAVRLHYGL 531 AIPRLVQLLV 581 RDVHNRIVIR 631 EAEGATAPLT 681 LFRTEPMTWN 731 DPMMDHDMGG


1

2

3

4

Positive selection

SI

5

6

7

Purifying selection


41 TTAPSLSGKG 91 QRVRAAMFPE 141 YQDDAELATR 191 PQMVSAIVRT 241 KMLGSPVDSV 291 KFLAITTDCL 341 RVLKVLSVCS 391 ATKQEGMEGL 441 GGIEALVRTV 491 PVVVKLLHPP 541 RAHQDTQRRT 591 GLNTIPLFVQ 641 ELLHSRNEGV 691 ETGDLGLDIG 741 HHPGAEYPVD

Figure S2

Gene: daxx

1 XXXXXXXXXX 51 XXXXXXXXXX 101 XXXXXXXXXX 151 XXXXXXXXXX 201 XXXXXXXXXX 251 ESRLCPPDYS 301 RHLDMVYNFG 351 XXXXXXXXXX 401 XXXXXXXXXX 451 XXXXXXXXXX 501 XXXXXXXXXX 551 XXXXXXXXXX 601 XXXXXXXXXX 651 XXXXXXXXXX

11 XXXXXXXXXX 61 XXXXXXXXXX 111 XXXXXXXXXX 161 XXXXXXXXXX 211 XXXXXXXXXX 261 DILRVVRRAD 311 SHLTDGYQPA 361 XXXXXXXXXX 411 XXXXXXXXXX 461 XXXXXXXXXX 511 XXXXXXXXXX 561 XXXXXXXXXX 611 XXXXXXXXXX 661 XXXXXXXXXX

21 XXXXXXXXXX 71 XXXXXXXXXX 121 XXXXXXXXXX 171 XXXXXXXXXX 221 XXXXXXXXMV 271 ERHGLGLSRR 321 TDPALADPTL 371 XXXXXXXXXX 421 XXXXXXXXXX 471 XXXXXXXXXX 521 XXXXXXXXXX 571 XXXXXXXXXX 621 XXXXXXXXXX 671 XXXXXXXXXX

31 XXXXXXXXXX 81 XXXXXXXXXX 131 XXXXXXXXXX 181 XXXXXXXXXX 231 TDSSLSPLPP 281 QLTQIAQDAF 331 DRRLRTNRTV 381 XXXXXXXXXX 431 XXXXXXXXXX 481 XXXXXXXXXX 531 XXXXXXXXXX 581 XXXXXXXXXX 631 XXXXXXXXXX 681 XXXXXXXX


1

2

3

4

Positive selection

SI

5

6

7

Purifying selection


41 XXXXXXXXXX 91 XXXXXXXXXX 141 XXXXXXXXXX 191 XXXXXXXXXX 241 AQIDKFINSQ 291 RDTGNSLQER 341 ALISLDDVIX 391 XXXXXXXXXX 441 XXXXXXXXXX 491 XXXXXXXXXX 541 XXXXXXXXXX 591 XXXXXXXXXX 641 XXXXXXXXXX

Figure S2

Gene: dna a1 1 MVKETGYYDV 51 AYEVLSDSKK 101 RERRGKNVVH 151 CPMCRGSGMQ 201 KIVRQKKILE 251 VYTRQGEDLI 301 RKCIMNEGMP 351 EETDDTENMD

11 LGVKPNASAD 61 RELYDRGGEQ 111 QLTVSLEDLY 161 VRLHQIGPGM 211 VHIDKGMKDG 261 MNLEIKLVEA 311 FHRRPFEKGR 361 DLYIYADLED

21 ELKKAYRKLA 71 AIKEGGMGGG 121 NGATRKLAVQ 171 VQQISTICVG 221 QKITFHGEGD 271 LCGFQKPIKT 321 LIVLFTVNFP 371 CDLSQERPHF

31 LKYHPDKNPN 81 GFGSPMDIFD 131 KNVICDRCEG 181 CQGQGQRISQ 231 QEPGLEPGDI 281 LDDRILLLTS 331 EENFLPLDKL 381 DDDEYHSSGG


1

2

3

4

Positive selection

SI

5

6

7

Purifying selection


41 EGEKFKQISQ 91 MFFGGGGRMH 141 RGGRRGVVEC 191 KDRCKACNAR 241 IIVLDQKVHP 291 HPGEVIRPGD 341 TQLERYLPER 391 VQCQTS

Figure S2

Gene:

1 MQFEIAIVLS 51 SNCTVVMENL 101 IIRGHILYQN 151 GVKFTGNPFL 201 GSCWAPGPSN 251 DCLACRDFQD 301 HNYVVTDHGS 351 NVLSINASNI 401 TVKEITGFLL 451 SLGLRSLKEI 501 TECSALTQTC 551 REFIMDKKCI 601 SGIPGENDTF 651 AAGVVGGLLV 701 EAPNQALLRI 751 LREATSPKAN 801 CLLDYVKEHK 851 TPQHVKITDF 901 VWSYGVTVWE 951 MVKCWMIDAD 1001 0 SI

11 SLLTLGCCSI 61 EITYVEKDYD 111 SYALAVLSNF 161 CNAETIQWYD 211 CQTLTKLNCA 261 EGTCKQVCPQ 311 CVRTCTANTH 361 DSFRNCTKIN 411 IQAWPENMTS 461 SDGDVVIRGN 511 DELCTSEGCW 561 ECDPECMPQN 611 IWKYADEKKV 661 TVIIALAIFI 711 LKETEFKKIQ 761 KEILDEAYVM 811 DNIGSQYLLN 861 GLAKLLSADE 911 LMTFGSKPYD 961 SRPRFRELIA 1011

r

21 QDKRVCQGLS 71 LSFLKSIREV 121 DKQSSVNKNQ 171 IVDKSKNPEM 221 EQCSHRCKGP 271 LMLYNPNTHQ 321 EVDENGVRKC 371 GDVSILPVAF 421 LSPLENLEII 471 PHLCYTNADQ 521 GPGPSMCFSC 571 GTQTCTGSGP 621 CQLCHPNCTQ 671 LMRRRYIKRK 721 VLGSGAFGTV 771 ASVNNPHVCR 821 WCVQIAKGMN 871 KEYHADGGKV 921 GIPASEIAGI 971 EFSKMARDPP 1021

31 NKLTLLGTSQ 81 GGYVLIALNK 131 SSNVGLQELS 181 FLIFANNTLN 231 KPSDCCNEHC 281 LEMNPDGKYS 331 KKCEGPCPKA 381 RGDSYTKTPV 431 RGRTKQHGTV 481 WKRLFKLEKQ 531 QHFMRQQQCV 581 DKCAECAHFK 631 GCTGPGLAGC 681 RTLRRLLQER 731 YKGLWIPEGE 781 LLGICLTSTV 831 YLEERHLVHR 881 PIKWMALESI 931 LEKGERLPQP 981 RYLVIQGDER 1031


41 DHYNNIVRMY 91 VSRIPIDNLR 141 LKSLTEILKG 191 CKKCDPNCFN 241 AAGCTGPRST 291 FGATCVKSCP 341 CNGLGMGNLV 391 LDPSKLDVFK 441 SVAAVNIDIT 491 NARVSENADP 541 NACNVLEGLP 591 DGPHCVHKCP 641 DHQTSQLSSI 691 ELVEPLTPSG 741 DVKIPVAIKV 791 QLITQLMPYG 841 DLAARNVLVK 891 LHRIYTHQSD 941 PICTIDVYMI 991 MHLPSPTDSK 1041

Figure S2 FYRTLIDGDE MDDVVDADEY LVPYNGFFNS PSTSRMQLLH SMSLNSSMGS

1051 CTIRNGQGYP 1101 MNPIYQDSVV 1151 FDNPHYCDQK 1201 QAEVH

1061 MREDSFIQRY 1111 PISAVTRAQN 1161 VTHQTSLDNP

1071 ITDPTDGAFE 1121 ADSQYLNSFS 1171 DYQQDFFPPK

1081 KDFQPVPEYV 1131 NTADFHEYLN 1181 SKVNGHLPAA


1

2

3

4

Positive selection

1 SI

5

6

7

Purifying selection


1091 NQNGNPVSDV 1141 TVQPALPRPL 1191 ENTEYLALSA

Figure S2

Gene: 1 MTERFDCHYC 51 SKDLSYKDRH 101 CHECKKTIMP 151 VPCYEKQFAM 201 TSRDDFAYCL 251 CKKCSVSLVG

11 KESLFGKKYI 61 WHEDCFHCFQ 111 GTRKMEHKGN 161 QCVQCKKPIT 211 NCFCNLYAKK 261 RGFLTERDDI

21 LREENPYCVK 71 CKRSLVDKPF 121 SWHETCFTCH 171 SGGVTYHEQP 221 CAGCTNPISG 271 LCPECGKDI

31 CYESLYSNAC 81 SAKDELLLCT 131 RCQQPIGTKS 181 WHKDCFLCTG 231 LGGSKYISFE


1

2

3

4

Positive selection

2 SI

5

6

7

Purifying selection


41 EECKKPIGCN 91 ECYSNEYSSK 141 FIPKDAHNYC 191 CKKQLSGQRF 241 ERQWHNDCFN

Figure S2

Gene: 1 MTAEEVNAEG 51 VHYVGTLLDG 101 LICKPEYAYG 151 ATKGEGYSKA 201 EKALQSMEKG 251 AKESWEMNTD 301 GLSEEYENKA 351 ALFRRGEALF 401 EKDKRLYANM 451 QEQTAA

11 QQTTQMEGED 61 TKFDSSRDRS 111 SAGSPPKIPP 161 NEGATVEVSL 211 EESLITLSPK 261 EKLEQSVIVK 311 KALRLAAHLN 361 AMKEFEQARD 411 FQKFAERDAK

b

21 ITPKKDGGVL 71 EKFSFDLGKG 121 NSTLVFEIEL 171 EGTFEGRVFD 221 YGFGTAGNSQ 271 EKGTQYFKEG 321 LAMCYLKVQE 371 DFQKVVQLYP 421 KEAEKQKDTK

31 KSIKKEGTGD 81 QVIKAWDIGV 131 FGFQGEDLTD 181 QRELKFEIGD 231 FNIPPDAMLN 281 KYKQASVQYK 331 HSQAVENCNK 381 SNKAAKTQVV 431 KQENTEGQNG

41 ENPMIGDKVF 91 ATMKIGEVCQ 141 DEDGGIIRRI 191 GESLGIPPGV 241 YKIKLISFEK 291 KIVSWLEHES 341 ALELDSSNEK 391 VCQRQIKEQH 441 DEMDIDQNET


1

2

3

4

Positive selection

3 SI

5

6

7

Purifying selection

Likelihood ratio test between the null model (no positive selection) and the alternative model (enabling positive selection) shows a significance level of: 0.05


Figure S2

Gene: 1 MSSPHPRLNQ 51 TFTRWCNEHL 101 TFRQMQLENV 151 YSISMPMWDE 201 ALGALVDSCA 251 IVDPNVDEHS 301 VVMKKAEFTV 351 IPKVTGTHKV 401 IANKTTYFDV 451 KPTKEGVHTI 501 VKETADFKVY 551 TTGNYTITIT 601 DFVVEAVGDD 651 HVLCNNEDIQ 701 FTVDAKQGGK 751 VMVSWGGVNI 801 DCSEAGQGDI 851 SYTIMVLFAD 901 FTVNTKGAGK 951 MGVNVTYGGD 1001 SI

11 SSAPSSAAVS 61 KCVNKRIANL 111 SVALEFLDKE 161 EEDDDVAKQK 211 PGLCPDWDSW 261 VMTYLSQFPK 311 ETISAGMGEV 361 TVLFAGLHIS 411 YTAGAGIGEV 461 YITFAGSQIS 511 TKGAGTGDLK 561 WGGQQIPRSP 611 VGTLGFSVEG 661 YSPFMAEIKP 711 APLKIQAQDG 761 PDSPFRMSIG 811 SIGIKCAPGV 861 QAIPMTPFRI 911 AKLDVQFTGP 961 SIPKSPFSVG 1011

a

21 NAALADKDAD 71 QTDLSDGLRL 121 NIKLVSIDSK 171 TPKQRLLGWI 221 DQTKPVDNAR 271 AKLKPGAPLR 321 LVYVEDPAGH 371 KSPFDVDVGM 421 GVSIVDPTGK 471 KSPFTVTVGE 521 VTIKGPKGLE 571 FEVKIGTEAG 621 PSQAKIECDD 671 SPGKDFHPEK 721 DGNPVDVQVK 771 AGSHPNKVKV 821 VGPAEADIDF 871 KVDPSHDASK 921 TKADAVKDFD 971 VAPSLDLSKI 1021

31 MPATEKDLAE 81 IGLLEVLSQK 131 AIVDGNLKLI 181 QNKLPQLPIT 231 EAMQQADDWL 281 PKLNPKKARA 331 REEAKVTANN 381 SQGDASKVTA 431 KDTVECNIED 481 ACNPSLCRAK 531 EPCKKKDLGD 581 PQKVRAWGPG 631 KGDGSCDVRY 681 VKAYGPGLQS 731 DNGNGTYSCF 781 SGPGVAKTGL 831 DIIRNDNDTF 881 VKAEGPGLSR 931 IVNNHDNTYT 981 KVSGPGEKMT 1031


41 DAPWKKIQQN 91 KMFRKYNQRP 141 LGLIWTLILH 191 NFSRDWQSGK 241 GIPQVITPEE 291 YGPGIEPTGN 341 DKNRTYSVVY 391 QGPGLEPSGN 441 KGNSSYRCTY 491 GRGLQPKGLR 541 GVYSFEYYPT 591 LEGGVVGSSA 641 WPTEAGEYAV 691 TGLAMSKPAE 741 YTPRKPLKHT 791 KAFEPTYFTV 841 TVKYTPPGAG 891 SGIEWNKPTH 941 VKYTPVQQGN 991 VGKDQEFTVK 1041

Figure S2

SKGAGGQGKV 1051 LTYDGAPIPG 1101 AGPAELTIEI 1151 QDVPNFPARL 1201 SGGNHIKTRI 1251 APVPNSPFRV 1301 LGLAVEGPSE 1351 FSVPVHDVVD 1401 GPKGIVEPVE 1451 VLPTHDASKV 1501 GKPKKANIRD 1551 TGDASKCTVT 1601 CTPDGTEVDV 1651 TALDGAPTEQ 1701 LVIPFTIKKG 1751 DIKYDGIHIP 1801 AGEGGLSLAI 1851 IPGSPFVAKI 1901 REEPCLLKML 1951 EIGDASRVRV 2001 NTEDQEDGTC 2051 SITRRRRAAS 2101 GENNTYCIRF 2151 SI

AAKVTGPSGK 1061 SPFPVEAVAP 1111 ISDNGTEAEV 1161 TVEPAVDSTG 1211 NNPSGNRTDA 1261 PVTEGCDPAR 1311 AKMSCTDNKD 1361 ASKVKCLGQG 1411 VVDNGDKTHT 1461 KASGPGLNTT 1511 NQDGTYLVSY 1561 VSIGGHGLGA 1611 DVVENEDGTF 1661 MLQQTQVPQY 1711 EITGDVRMPS 1761 GSPLQFYVDY 1811 EGPSKADISC 1861 TGDDSMRMSH 1911 RNGHVGISFV 1961 SGPGLSEART 2011 KVTYCPTEPG 2061 VANVGSQCDL 2111 VPTEMGVHTV 2161

PVPCKVEPSL 1071 ADPSKVRCSG 1121 HIQDNGDGTY 1171 VKVFGPGVGN 1221 LIRDLGDGTY 1271 VRVHGPGLQS 1321 GSCSVEYVPY 1371 LGNNVRANIP 1421 VSYVPTREGP 1471 GVPASLPVEF 1521 VPDMTGRYTI 1571 GVGPTIQIGE 1621 DIFYTAPQPG 1671 AYAPGVGQPW 1721 GKIAKPDITD 1771 VNSGHVTAYG 1821 TDNQDGTCTV 1871 LKVGSAADIP 1921 PKEIGEHLVN 1971 FEPAEFIIDT 2021 NYIINIKFAD 2071 SLKIPEINIG 2121 SVKYQGQHVP 2171

SPETSQVRFI 1081 PGLERAKVGE 1131 TITYIPLYPG 1181 KGVFREATTD 1231 QVEYTPYEEG 1281 GITNKPNKFT 1331 EPGTYNLNIT 1381 QSFTVDTSKA 1431 YSVSVLYADE 1481 TIDAKDAGEG 1531 LIKYGGDDIP 1581 ETVITVDAKA 1631 KYVICVRFGG 1681 ATDRPVGMNG 1731 NKDGTVTVKY 1781 PGLIHGMVNK 1831 SYLPVLPGDY 1881 LDIGELDLSQ 1931 IKKNGRHIPS 1981 REAGYGGLSL 2031 QHVPGSAFTV 2081 DMTAQVTSPS 2131 GSPFQFTVGP 2181


PREQGPYEVE 1091 TGKFNVDCTN 1141 VYTITIRYGG 1191 FTVDARALTK 1241 VHNVEVCYDD 1291 VETRGAGTGG 1341 YGGQPVKGSP 1391 GVAPLQVRVQ 1441 EIPRSPFKVK 1491 LLAVQITDPE 1541 YSPYRIRALP 1591 AGKGKVTCTV 1641 EHIPNSPFQV 1691 LDVAGLRPFD 1741 APTEAGLHEM 1791 PAIFTVNTKD 1841 NILVRYNDKH 1891 LTASLTTPSG 1941 SPITVMINQS 1991 SIEGPSKVDI 2041 KVTGEGRMKE 2091 GKVHKAEIME 2141 LGEGGAHKVR 2191

Figure S2

AGGPGLERAE 2201 SGVSYIVQEP 2251 SGLKVNQPAS 2301 IPRENGLYLI 2351 NTGSPCEFIV 2401 GNYLISIKYG 2451 ATMQQGAPAW 2501 GVDGPKVPCE 2551 HISVP

AGIPAEFSIW 2211 GDYEVSIKFN 2261 FAVSLNGAKG 2311 DVKFNGSHIP 2361 NTSSAGPGAL 2411 GPYHIVGSPY 2461 ASSDASHVVA 2511 EILVKHLGNR

TREAGAGGLS 2221 DEHIPDSPFI 2271 VIDAKVHSPS 2321 GSPFKIRVGE 2371 AVTIDGPSKV 2421 KAKITGPRLV 2471 KGLGLTKGFV 2521 LYNVSYQLKE

IAVEGPSKAE 2231 VPVASPSDDA 2281 GALEECCVTE 2331 TGQAGDPGMV 2381 KMDCQECPEG 2431 SSHSLHETSS 2481 GQKNSFSVDC 2531 KGDYILVVKW


1

2

3

4

Positive selection

SI

5

6

7

Purifying selection


IAFEDRKDGS 2241 RRLTVASLQE 2291 IDEDKYAVRF 2341 SAYGAGLEGG 2391 YKVIYTPMAP 2441 VLVDPISRSS 2491 SKAGRNMLLV 2541 GDEHIPGSPF

Figure S2

Gene: 1 MTEQMTVRGT 51 NYGIPQRALR 101 FVGHTKDVLS 151 VSCVRFSPNS 201 SPDGSLCASG 251 ATGPSIKIWD 301 GYTDNLIRVW

11 LKGHNGWVTQ 61 GHSHFVSDVV 111 VAFSADNRQI 161 SNPIIVSCGW 211 GKDGQAMLWD 261 LEGKIIVDEL 311 QVTIGTR

b 1

21 IATTPQFPDM 71 ISSDGQFALS 121 VSGSRDKTIK 171 DKMVKVWNLA 221 LNEGKHLYTL 271 RQEVISTSSK

31 ILSASRDKSI 81 GSWDGTLRLW 131 LWNTLGVCKY 181 NCKLKTNHIG 231 DGGDTINALC 281 AEPPQCTSLA


1

2

3

4

Positive selection

SI

5

6

7

Purifying selection


41 IMWKLTRDET 91 DLTTGTTTRR 141 TIQDESHTEW 191 HTGYLNTVTV 241 FSPNRYWLCA 291 WSADGQTLFA

Figure S2

Gene: r 1

1 MERFLGFVKQ 51 PYTKPSNPSK 101 IDKDGKPRVS 151 KNVGERVVLE 201 EDRNKSRPVV 251 ILKQCGQEAT 301 YCNKQVIVID 351 ASACEHVKLE 401 YQHYNTYHPD 451 TLPRNMYPTS 501 TLVGDPILGF 551 ILAINGIPTE 601 VKLPKKPGVE 651 LAIDNIRLDN 701 VELKRYGGPL 751 NSNSLKGKPL 801 DVEDESQAAQ 851 ASGYSFHSHE 901 VGNDGTEPDQ 951 QPQRSLLGRQ 1001 SI

11 IRRSRRRKGK 61 PPDGALAVRR 111 NLRQGGIAAR 161 VEYELPPISV 211 ITTVRPGGPA 261 LLIEYDVSVM 311 KVKPASIADR 361 ILPHHQTRLP 411 HSRTQASKYQ 461 PRGTLMRRKL 511 GIQLQGGVFA 561 DSTLEETNQL 611 LGITISSPSS 661 CSMEDAVQIL 711 GITISGTEEP 761 SEAIHLLQMA 811 KTGKLSDMYS 861 WRNAKSRGSL 911 EENFWSQALE 961 ASFQERSLSR 1011

21 KYRPEEDYHE 71 QSIPDEFKGS 121 SDQLNVGDYI 171 QGSGVIFKNV 221 DREGTVKSGD 271 DSIATASGPL 321 CGALHAGDHI 371 LKGSDHVKVQ 421 KPSPNNLPLV 471 KKKDHKSSLS 521 TETLSSPPLI 571 LRDSSITSKV 621 RKPGDPLIIS 671 QQCEDLVKLK 721 FDPIIISSLT 771 GESVTLKIKK 821 TTIPSVDSAV 871 SPVSRQRNNI 921 DLETCGQSGI 971 PQYTPTNRSN 1021

31 GYEDVYYYAS 81 TIVELMKKEG 131 KSVNGINLTK 181 EVTLHKEGNT 231 RLLSIDGIRL 281 LVEVAKSPGS 331 LSVDGTSMEY 381 RSNRQLPWDS 431 SSSFSPTSMS 481 LASSTLGLAG 531 AYMDPDSPAE 581 TLEIEFDVAE 631 DIKKGSVAHR 681 IRKDEDNSDE 731 KGGLAERTGA 781 QGEATSPKKP 831 ESWDGSGIDT 881 FQDIGLSDDE 931 LRELEATIMS 981 TLPTEAGRKA 1031


41 EHLTFVRDEG 91 TTLGLTVSGG 141 FRHDEIISLL 191 FGFVIRGGAH 241 HGTSHAEAMS 291 SLGIALTTSM 341 CTLAEATQLL 391 CANNNRNFLP 441 AYSLSSLNMG 491 QVVHTETTEV 541 RSGILQIGDR 591 SVIPSSGTFH 641 TGTLELGDKL 691 QESSGAIIYT 741 IHIGDRILAI 791 SASGRLSELS 841 VFGTQVPGYQ 891 WDRPTTSGFT 941 GSTMSLNHEP 991 FAMRKIKQEM 1041

Figure S2

KDIMSPTPVE 1051 LGGLKPYDRL 1101 VTELDQQPSE

LHKVTLYKDT 1061 LQINHVRTRD 1111 APSEWSEQND

DAEDFGFSVS 1071 FDCCLVVPLI 1121 ALQQPQQQQS

DGLLEKGVYV 1081 AESGNKLDLV 1131 SRLAGVDARE


1

2

3

4

Positive selection

5

6

7

Purifying selection


NNIRPSGPAD 1091 ISRNPLASQP 1141 PTKTL

Figure S2

Gene: a

1 MADTSMEIVE 51 FNKRLDEWVT 101 DLNVQAASAP 151 SVYPAARETF 201 EMIKVFQYNS 251 ITRMKNIDCI 301 LQRHLTKCNL 351 HKTLYYDTDP 401 YQRRGYGKLL 451 LMDLKSDNGE 501 LSEDIVDGHE

11 GCRLPVLRKN 61 PDRLDMKKLQ 111 SRGKTLPTPK 161 TTKTREDEPL 211 PRTTSGCLPP 261 ELGRHRLKPW 311 RHPPGNEIYR 361 FLFYVMTEYD 411 IEFSYELSKV 461 RPQITINEIS 511 RAMQKRHLRI

21 QENEDEWPLA 71 FPKKEAKTPT 121 RKAETVSLAS 171 TSITTVTNGT 221 GEDSQDSSDG 271 YFSPYPQELT 321 KGTISFFEID 371 CKGFHIVGYF 421 EGKTGTPEKP 471 EITSVKKEDV 521 DPKCLHFTPK

31 EILSVKDTLG 81 KNGLPGSRPS 131 QVTPATSVPS 181 TRRVLPPSQP 231 IPTAPRMTGS 281 TLPILYLCEF 331 GRKNKTYSQN 381 SKEKESTEDY 431 LSDLGLLSYR 481 ISTLQYLNLI 531 DWSKRGKW


1

2

3

4

Positive selection

0 SI

5

6

7

Purifying selection


41 RKLFYVHYID 91 SPEREVRKSL 141 LPSSAEATQA 191 GRKRKTCGTD 241 LVSDRSHDDI 291 CLKYLKSLKC 341 LCLLAKCFLD 391 NVACILTLPP 441 SYWSQTILEI 491 NYYKGQYILT

Figure S2

Gene:

1 MEDRQGDESY 51 YEKDGKLYCR 101 KVVIEERDTY 151 LISVPAATNG 201 DRILEINGVP 251 PRSRLRVPGA 301 PASPKEYPGL 351 IKVTHKATGE 401 YKDKRLNLIT 451 SIIHRDLNSH 501 RRIDRKKRYT 551 DPECLPRTLD 601 KLVDCFDALA 651 PASASLGENG

11 RCVGCGSRIL 61 KHYWENFGES 111 ALVERSKLYC 161 KRGLSVSVIG 211 VGTLMEEEVE 261 SRLRLPSPAD 311 FRDISRSESL 361 VMVMKELIRC 411 EFIEGGTLKD 461 NCLVKLDNTV 511 VVGNPYWMAP 561 FGLNVRKFLE 611 LNLELGIPLP

21 DTFYIKVLQD 71 CHGCSLLMTG 121 GTCHQQIVLT 171 DCSGGTTSVQ 221 DLIQRTNQTL 271 PVLESRETLE 321 RSSTSCSHRI 371 DEETQKTFLK 421 FIRDMDPFPW 471 VVADFGLSRL 521 EMLNGKRYDE 571 KFLPEDCPSA 621 AELEVLHHHL

31 VWHNSCFQCS 81 PVMAAGEYKY 131 PVLEKRSSVL 181 VKEVLGMHIS 231 QLVIEYDPVR 281 DSTLKRRSLR 331 FRPCDLIHGE 381 EVKVMRSLEH 431 EQRVSFAKGI 481 IVEEKSRAPP 531 RVDIFSFGIV 581 FFPLAVACCD 631 CGAHSPVGAD

S


1

2

3

4

Positive selection

1 SI

5

6

7

Purifying selection


41 ECCDHLTNWY 91 HPECFVCLSC 141 ACDSLPHTVT 191 PEVRNAIHAG 241 QRLDRLRLGS 291 RSNSICKSPG 341 VLGKGFFGQA 391 PNVLKFIGVL 441 ASGMAYLHSM 491 EKQSAKKRTF 541 LCEIIGQVYA 591 LVPENRPTFE 641 LPGSGPPVRH

Figure S2

Gene: 1 MATAAVSGAA 51 AYDKENKVRV 101 APSIDQMKDV 151 SANVLHRDLK 201 WYRAPEIMLN 251 GILGSPSQED 301 KMLTFNPHKR 351 TLKELIFEET

11 GGAPNTGSGA 61 AIKKISPFEH 111 YIVQDLMETD 161 PSNLLLNTTC 211 SKGYTKSIDI 261 LNCIINIKAR 311 IEVEEALAHP 361 ARFQPGYRS

a

1

21 ELVRGQAFDV 71 QTYCQRTLRE 121 LYKLLKTQHL 171 DLKICDFGLA 221 WSVGCILAEM 271 NYLLSLPLRN 321 YLEQYYDPTD

31 GPRYSNLSYI 81 IKILLRFKHE 131 SNDHICYFLY 181 RVADPDHDHT 231 LSNRPIFPGK 281 KVPWNRLFPN 331 EPVAEAPFKF


1

2

3

4

Positive selection

2 SI

5

6

7

Purifying selection


41 GEGAYGMVCS 91 NIIGINDIIR 141 QILRGLKYIH 191 GFLTEYVATR 241 HYLDQLNHIL 291 ADPKALDLLD 341 DMELDDLPKE

Figure S2

Gene: 1 MAESGSSAAA 51 DVGPRYTDLQ 101 REIKILLRFH 151 QLSNDHICYF 201 LARIADPEHD 251 EMLSNRPIFP 301 KPKIPWNKLF 351 SDEPVAEEPF

11 AGAAGSNSSA 61 YIGEGAYGMV 111 HENIIGINDI 161 LYQILRGLKY 211 HTGFLTEYVA 261 GKHYLDQLNH 311 PKADNKALDL 361 TFNMELDDLP

a

21 AGPGGAVAPG 71 CSAFDNVNKI 121 LRARHIDYMR 171 IHSANVLHRD 221 TRWYRAPEIM 271 ILGVLGSPSQ 321 LDRMLTFNPL 371 KEKLKELIFE

31 GPSGAAGSKP 81 RVAIKKISPF 131 DVYIVQDLME 181 LKPSNLLINT 231 LNSKGYTKSI 281 DDLNCIINMK 331 KRINVEQALA 381 ETARFQANYQ


1

2

3

4

Positive selection

3 SI

5

6

7

Purifying selection


41 GLESVKGQNF 91 EHQTYCQRTL 141 TDLYKLLKTQ 191 TCDLKICDFG 241 DIWSVGCILA 291 ARNYLQSLPQ 341 HPYLEQYYDP 391 GS

Figure S2

Gene:

1 MAAVSGVVIS 51 LLERLHAKHC 101 LKVSSLPAMT 151 QLVDVKVAHH 201 LKTKMYLALQ 251 LVTLQCYVSP 301 PIAPLITGTH 351 HRMGNATGIP 401 LPGQQHCYFL 451 YNTLIGSCVK 501 MEVLDSRQVS 551 TIQADTPALS 601 GNTPTGGGGS 651 EPMSQAGGAQ 701 PTQAPPAAGH 751 SPLERQNSSG 801 MGLKPQGSLP 851 LDTPHSITPA 901 PSGPSRMVRL 951 GGDDGGALGT 1001 SI

11 GCSPARELGP 61 ASRPWQETSK 111 DRLESIARQN 161 GENPASCPEL 211 SLEMDLTKMM 261 YDVFEEETGA 311 PVDNKGTPSF 361 LFETAPPLAP 411 NRDAPVQDGR 461 RTVLKEDTPG 511 CKLYKGLSDA 561 LIAETVEDMV 611 SAGAAGGGGG 661 QQQAPLQQPA 711 QPHHTPPPAS 761 SPRTDIMGGG 811 LALQHHQHHQ 861 PSQCGTPPTG 911 SSSDSIGADI 961 PIRDSSSSGQ 1011

1

21 GAPTVGPPTI 71 VVRQAMEKRN 121 GLGSHLSPSG 171 VQHLRERNFE 221 HMFRLATNAN 271 LLNLTDSNVP 321 SSVTNSNCVD 371 LYELITQSQL 421 CLQGALVTKV 471 LLQFEVCPLT 521 LICTDDFITK 571 KKNLPPAGSP 621 AGASFPGPIS 671 QQGHGDDFSK 721 SPASNTKNHP 771 SCGGGGGVSG 821 LEDDFHRELF 871 PGVPYLSQGP 921 NEILSDIPEQ 971 GSAVFEADLF 1021

31 GDRPRPEEGT 81 VLNAGGHQLL 131 TECYITSDMF 181 EFSKHLKGLV 231 TVETILHGSV 281 RNLGVGVSVT 331 LPACFFLKLR 381 QEEGGGALPP 431 PFRHPAQVPA 481 DSSFSVSFQH 531 VVQRCMSIPV 581 GYGMGTGGGG 631 TLFGMGLALK 681 VTQNPILTSL 731 MLMNLLKDNP 781 GKTKKKRQRN 831 SMDVDASQNP 881 PQSQSQQQQQ 931 AGKMAAGGGG 981 SAGSNENPFT 1031


41 EAEKQSRVGA 91 LTCLETLQRA 141 YVEVQLDSGG 191 NLYKLPGDNK 241 GLVTARSGGH 291 IEGTSSVYKL 341 RPLPFSLSFI 391 LAHNMRFYAS 441 LLDIIRHQAA 491 PVNESLVCVV 541 TMRAIRRKAE 591 NLMGIPGVGG 641 ERHEGRGPGG 691 LQITGNVGSS 741 SQDFSSLYSS 791 PDKAGGMGGA 841 IFDVNLPGDG 891 QQQVAPPQPP 941 GHGPHHHGLG 991 DPVDLIADAA 1041

Figure S2

TAATPNSDSS 1051 KGFGGGSQQH 1101 LLGGPLPAPD 1151 GGKEGNGGGG 1201 LDPEGKSPSH 1251 GGATPPIPKI 1301 SHHSHSSSSS 1351 SQSKGSSQGM 1401 ASLINPNIKP 1451 GSGGGGLGSG 1501 SSSSSSFSAG 1551 DKLKHGVGTG 1601 VSSTGVAKII 1651 PLFSASTPKH 1701 DDDQALRPLQ 1751 EKKKSSSSCS 1801 RTEDDDLMDS

SNNFFPDTVD 1061 TPAGTPQNPT 1111 LADSHSGGGQ 1161 GGGSGLGGAS 1211 SSGGRPYTPP 1261 TIQIPKGTLT 1311 SSSGKMKGSK 1361 GGGKPGSSPI 1411 NISPSHSRGV 1461 SKTSSGSGMG 1511 SQSQYGGGGG 1561 GHGGEYMSKR 1611 ISKPDGGSPS 1661 DRCSPSHGRS 1711 PPHEYMSSMP 1761 TSSSHPLKAD 1811 ALTGNLDSFK

FNPELLAGPG 1071 PHGRSTPDPS 1121 SPLMMMGMGG 1171 GGSSEGKQGK 1221 SGIGGSGGGS 1271 GGKTSSHGGY 1321 SDGSLGQGGG 1371 TKHGLAGAGV 1421 GAPDKLSSPM 1471 PQKQQMGGTS 1521 GGGGGGGNNN 1571 DKGDKESKSK 1621 IKAKVTLQKP 1671 PGYTPLNPDS 1721 ISSGEKHKKH 1771 SWSRSPIAAP

FPQAYFEDSS 1081 MKDPFEMSMV 1131 GGGSDFKSDA 1181 RSRTPSSDGK 1231 MGAGGGSKSP 1281 TSSSSAGGGG 1331 SKPGGGGGGC 1381 VAGGGVGGGA 1431 KLQQQQVPGT 1481 SSGSSSSSSS 1531 PNAKGKSPSR 1581 VSMSGVGSGD 1631 GEGSGEAMRS 1681 ESESGSSSVA 1731 KKEKKKQKER 1781 DPSLSLLGSD


1

2

3

4

Positive selection

SI

5

6

7

Purifying selection


PSADGDLDLV 1091 FGGSGGGGKP 1141 KAKQQQLMRG 1191 SKDKPPKRKK 1241 GSSGRSQTPP 1291 GGAAGGGGSK 1341 SGGGGGGGGG 1391 KMKPQGGKPP 1441 PPSSKAKSPM 1491 SSSSSSSSSS 1541 NKKPSLTAVI 1591 KKALDSKSGV 1641 QLSGPKAYGS 1691 EKSHQNSPSS 1741 ERERERDRDK 1791 RPARPSPAYL

Figure S2

Gene: 1 XXXXXXXXXX 51 XXXXXXXXXX 101 XXXXXXMVHT 151 VPGDPRRPYP 201 SPAAPTCLXX 251 XX

11 XXXXXXXXXX 61 XXXXXXXXXX 111 DVECALMVNV 161 TDLEMRSGML 211 XXXXXXXXXX

21 XXXXXXXXXX 71 XXXXXXXXXX 121 FVSGSISSEE 171 GHMSNLPTNG 221 XXXXXXXXXX

31 XXXXXXXXXX 81 XXXXXXXXXX 131 IIKYAHRISA 181 VNGHLPGDAL 231 XXXXXXXXXX


1

2

3

4

Positive selection

SI

5

6

7

Purifying selection


41 XXXXXXXXXX 91 XXXXXXXXXX 141 SNAVCAPLNW 191 AAGRLPGSLV 241 XXXXXXXXXX

Figure S2

Gene:

1 MAAFGILSYE 51 VSGDEHGSAK 101 NFWLVTARSQ 151 VPVMRAAWMI 201 KVAEFYRQSS 251 HEFLTWVLEC 301 TRRLNLLLSD 351 FTDFYICPQH 401 LLPIAPSNLP 451 ETTAGFTIGR 501 MNPDDDAVVT 551 VVDEKGSVSS 601 LVLLFCELIR 651 RKEQEAASSV 701 EKPAPEQDGK 751 NQRLVVLYGV 801 TKPEAFPTAE 851 PLVQHIQFIF 901 YTTGLCLCIV 951 ERCILAYLYD 1001 SI

11 HRPLKRPRLG 61 NVNFNPSKIS 111 SSINNWFTDL 161 KMTCAYYAAI 211 SQGCVSPLPS 261 FEKIRPGEDE 311 GTVGPGAGGH 361 RPLVFGLSCM 411 MPGGNTTFTQ 461 VLHTLEVLDS 511 LLCEWAVSCK 561 GSLSAATLPV 611 HDVFSHNIYM 661 KMEDAGLSES 711 STTKDKTLDP 761 GKQRDEARHT 811 DIFSKFQHLS 861 DLMEYSLNIS 911 AVLRRYHSCL 961 LYTSCSHLKS 1011

1

21 PPDVYPQDPK 71 SNFSSIIAEK 121 AGTKPLTQLA 171 TETKVKKRHV 221 TPVEVETAMK 271 LLKLLLPLML 321 QTHSITAQPG 371 LQSIVLCCPS 421 QVRAKVREIE 471 HSFEKSDFSN 521 RSGRHRAMVV 571 FQDVLLQFLD 621 CTLISRGDLA 671 MEIDHNSSAI 721 AFPLVYELPR 771 IKKITKDILK 821 HFDQHQVTSQ 871 GLIDFAIQLL 921 ILNPDQTAQV 971 KFGEIFSDFC 1021

31 QKEDELTALN 81 LRCNTFPDTG 131 KKVPIFSKKE 181 IDPCIEWTQI 231 QWEYNEKLAM 281 QYSGEFVQSA 331 NALPPTPTPQ 381 ALVWHYSLTD 431 EQVKERGQAV 481 SLDSLYNRIF 531 AKLLEKRQAE 581 TQAPMLTEPG 631 SDSHLPRPRS 681 FDDVMFSPPM 731 HIQYATHFPI 781 VLNRKSTAET 831 VSRNVLEQIT 881 NELSLVEAEL 931 FDGLRIVVKH 981 SKVKNSIYCN 1031


41 VKQGFNNQPA 91 KRKPQVNQKD 141 EVFGYLAKYT 191 ITKYLWEQLQ 241 FMFQDGMLDR 291 YLSRRLAYFC 341 PAGGNQPQTP 391 SRNKTGSPLD 441 EFRWSFDKCQ 491 GSGQSKDGHE 541 IEAERCGESE 591 NESERVEFSN 641 PSDEPSDESE 691 HCESKGSPSP 741 PQEESASHEC 791 GGEEGQKRKR 841 SFALGMSYHL 891 LLKSSSLVGS 941 GVNPADCSSA 991 IDPSDSNMLW 1041

Figure S2

DPVFMIETIA 1051 PERVNDIGIL 1101 DVSDLSFHDS 1151 GARLTCRILL 1201 IVVGAVFAVL 1251 SIETASLDVY 1301 RLLQLICYPH 1351 QSTNNELNSL 1401 SNNASKMKPV 1451 LGSSSRKERD 1501 VQQIVTNWRE 1551 WAVLLLDIIS 1601 EENKRAYMNL 1651 LIDTKGNKIA 1701 DRKVTKFEEQ 1751 KKLAEAVKPE 1801 AGMPPEMLHG 1851 TLPMRPNRPA 1901 QQLQAKLSQG 1951 HPSQTGGMVP 2001 YVHAMQNTPR 2051 VGIHSLFGLS 2101 QPQALGMQPL 2151 SI

NPSAHNFNHS 1061 CAELTAYCRS 1111 LATFVAILIA 1161 HLFKTPQRNP 1211 KAVFMLGDAE 1261 AKYVLKSICQ 1311 RQLDSEEGEN 1361 LENIAKATIE 1411 LSSSERSGVW 1461 RQKQKSMSLL 1511 DQYQDDCKAK 1561 SGTVDMQSNN 1611 VKKLRKELGD 1661 GFEKEGLQVS 1711 QRLLLYHTHL 1761 KSSAAVATDS 1811 QQGHPFNRMV 1861 AYPNMMTGMP 1911 MLGQQVRQMP 1961 PAYANQPFQG 2011 FAHQQASIIQ 2061 GHQACLLLHW 2111 PPQQPMFPRQ

MVGKILNDSP 1071 LSAEWLGVLK 1121 RQCLLLEDLV 1171 SPQDSSKSDK 1221 LKGSGFPHPA 1271 QEWVGERCLK 1321 PQRQRIKRIL 1371 VFQKSAEMIS 1421 LVAPLIAKLP 1471 SQQPFLSLVL 1521 QMMHEALKLR 1571 ELFTTVLDML 1621 RQSESLEKVR 1671 TKQKISPWDV 1721 KPKPRSYYLE 1771 SKKKSSKKKR 1821 YGPQSMGMYP 1871 GGVGNLITAL 1921 PNPSYGTLQP 1971 SHPAPNPAMV 2021 GLSHMPGQGV 2071 RAGAHVTVML 2121 GMQQTQQQQQ

ANRYSFVCNV 1081 ALCCSSNNGN 1131 RCVAIPSLLN 1181 PAVGIRSSCD 1231 GLDDTPEDDL 1281 SLSEDSSALQ 1331 QNMDQWTMRQ 1381 SNPLGNGSAV 1431 TTVQGHVLKA 1481 TCLKGQDEQR 1531 LNLVGGMFDT 1581 SVLINGTLAA 1631 QLLPLPKQTR 1681 FEGLKHSAPL 1731 PLPLPPEEEE 1781 NHSSSKTEDF 1831 QNQPLPPGGP 1881 DQQAYRAYKP 1931 TQVPPPQGYT 1981 DSLRQMQQRP 2031 HPGMRSNQML 2081 LCLYQTPFDQ 2131 TAALVRQLQQ


LMDVCVDHRD 1091 CGFNDLLCNV 1141 AACSEQDSEP 1191 RHLLAASQNS 1241 GSKKSGGRAV 1291 DPVLVNIQAQ 1341 SSLELQLMIK 1391 SGPIQGPVTN 1441 AGEELEKGQH 1491 EGLLTSLYSQ 1541 VQRSTQQTTE 1591 DMSSISQGSM 1641 DVITCEPQGS 1691 SWGWFGTVRV 1741 PPTPVAPEPE 1791 ASTQRGVPYT 1841 RLDTTYRPTR 1891 QPPIQGQILR 1941 SYGPHMGMQQ 1991 SGYIHQQAPG 2041 DFLRQQQALR 2091 VSAAQPPAQA 2141 QLSNTQPQQN

Figure S2

TNSFY


1

2

3

4

Positive selection

SI

5

6

7

Purifying selection


Figure S2

Gene:

1 MSSCFVPNGA 51 DPILCSFSRC 101 GEEEGAWESG 151 EKPINKSEHL 201 NSPFQVILSP 251 EDKPDDMDWE 301 CTAVYSGVHQ 351 VSDGFSTDST 401 TCEEESTDKA 451 QPPPKHKAVE 501 AQDGGEPLKN 551 SEAMEPTVYV 601 DLPGTGSQES 651 DHEPELDPYA 701 EGEDAMSLFS 751 SDEDELAPGA 801 SLEQHIMGYS 851 SPKPSEIKDF 901 RPSWTVGKLE 951 MSNSAPPSNG 1001 100 SI

11 SLEDCHSNLF 61 LKADVLSVWR 111 LSYECRTLLF 161 SCAFTFFLHG 211 FGLNGTLTGQ 261 DDSLAAVEVL 311 VPASTRDPAI 361 SHHGGKIPRK 411 GSWDFVDPTQ 461 KPEKGEKQQK 511 PATPHSQHFY 561 GAAVSPDEDN 611 VVSVTELMAT 661 FVDGDVEFSF 711 PSAKTEDAQR 761 RRAVNGTDEK 811 PMNMNSKEYG 861 SFVYKPEGCQ 911 LLNPVPALTF 961 GTGILPSPAT 1011

1

21 CLADLTGIKW 71 RHQTAGRREL 121 KAIHNLLERC 171 DSNVCTSVEI 221 SFKLSDPPTQ 271 VAGVRMVYPA 321 SSVTLTPPTS 371 LASQVVDRVW 421 RSNCNCSRHK 471 RPLTPFHHRT 521 QPAPEPCLVP 571 AHAPWKFFIL 621 SKNPLKVSEG 671 RDKKDKQGGE 721 SAAHNRTAST 771 FGNKEAKPAS 821 SLDNASGMTV 871 AFVGCSMFAP 921 LNKDGNIPSV 971 PRFSAPTPRT 1021

31 KKYVWQGPTS 81 WLFWWGEDPN 131 LMNRSFVRIG 181 NQHQPIYHLS 231 KLIEEWKQFY 281 CLVLVPQSDI 331 PEEAQTMDSQ 381 QECNINRAQN 431 NLKQRAGSTP 481 SICEDVSMEP 531 QKPAEDPRLD 581 PRKKDSDFAP 631 LVQMYIQRRT 681 REAGKKHKAD 731 SLMHENDLAV 781 LDQLSCISSA 831 LDGSSVLGGQ 881 LKTLPSQCLP 931 GSAMDQDYIQ 981 PRTPRTPRGP 1031


41 APILFPVTEE 91 FAELIHHELT 141 KWFVKPYEKD 191 EGHLTLAQQS 241 PISPSSKESS 291 PAVTPVGSSH 341 SAQKWVKFSS 391 KRKFSATTNG 441 GQPQAAGQPP 491 DATGQRLGMR 541 PLAQPFPPAY 591 PQLPGDKLRD 641 QYLSAAISDS 691 DGSNGGPVPA 741 SINDLDNLFN 791 DLHQMFPTPP 841 FKIEVEEGFC 891 PIKLPEECLY 941 TYTPQTHTPF 991 ASVQGSLKYE 1041

Figure S2

NSDLYSPAST 1051 CNFDSCCVCV 1101 SGLFLEDELD 1151 ILLLQDQCTN 1201 EHGRQFMDNM 1251 LQPVLQDAIQ 1301 TFLVGYEYDF 1351 AKGFFRDLTA 1401 FLKAASSNSD 1451 QSSSTPAPVV 1501 VGMGSSLQSS 1551 GAAQTQGPAE 1601 MEGGAQSSSV 1651 DERHIYAQHL 1701 ERPECLRLYT 1751 WLLATCTDLY 1801 QMTSLPWRVV 1851 SAADTPSILS 1901 PQDTSCTHIL 1951 DTGEDLVDPD 2001 EAPNILQQPL 2051 VSSVQSDELL 2101 SCLPIHFVVL 101 SI

PSTCRPLNSV 1061 CNMNIKGADV 1111 IIGRGSDASR 1161 PFSPITAPEP 1211 SGGKVDEALV 1261 KKRTVRSWGV 1311 VVLSPFGLPY 1361 VYESCRLGQH 1411 SFAKLKLYAQ 1461 SAPGSQGTLT 1511 KPSSFPPFGN 1561 PPESTMEREK 1611 WTLGLLRCYL 1661 KSLAFSVFSQ 1711 PPFILAPVKD 1761 GELLETCIIN 1811 IGRLGRIGHG 1861 ACLVAMEPQG 1911 VFPTSAFVQV 1961 IINILPASPT 2011 ALGYFVSTAK 2061 HSKHSHPLDS 2111 NQMYNFIMNM

EPATVPSIPE 1071 GVYIPDPNCE 1121 EVEKRFEAVH 1171 DSAPARGPGA 1221 KSTCLHHWAK 1271 QGPLTWQQFH 1321 WEKLLLDPFG 1371 RPISKTHPDG 1421 VCRHDLAPYL 1471 SSGTMTATAG 1521 MGAQSGSSQS 1571 VGVPTDGDSH 1621 EMLQSLPPHI 1671 CRRPLPISTN 1721 KQTELGETFG 1771 IDVPNRARRK 1821 ELRDWSILLS 1871 SFVIMPDSVS 1921 ANSNYTTENI 1971 TSPVHSPGSH 2021 AGPLPDWFWA 2071 NQTSDVLRFV

AHSLYVNLIL 1081 VQYSCTCGFS 1131 GSGASAERAG 1181 PPPCVRVEER 1231 RNAVDVSMLC 1281 KMAGRGSYGT 1331 SQRDVGYLVL 1381 IVRVGTAAAK 1431 AAQSLDSSLL 1481 TAIPPSASGT 1531 GTLGQQAGTQ 1581 AITYPPAIVV 1631 RNAVSVQIIP 1681 VKTLTGFGPG 1731 EASQKYNVLF 1781 KGSARRLGLQ 1831 RRNLQSLSRR 1881 TGSVFGRSTT 1931 DIAFNPINDG 1981 YPHGGDGSKG 2031 ACPQAQNQCP 2081 LEQYNALSWL

L


SESVMNLFKD 1091 AVMNRRYGNG 1141 SLRDQVPDDL 1191 DCYSDCYLAL 1241 SQDVLRVLLS 1291 DESPEPLPIP 1341 CPENEALLSG 1391 KLADQPVSDW 1441 VQPSPPPASS 1491 PSSTLPSSGP 1541 APGITGENVP 1591 YIVDPFTYEE 1641 CQYLLQPVKN 1691 LALDTALKSP 1741 VGYCLSHDQK 1791 KLWEWCLGLV 1841 LKEMCRMCGI 1891 LNMQTSQLNT 1941 SDGMGIFDLL 1991 QSTDRLESHE 2041 LFLKASLHLH 2091 TCDPATQDRR

Figure S2


1

2

3

4

Positive selection

102 SI

5

6

7

Purifying selection


Figure S2

Gene:

1 MAPVQIGSDG 51 RTYHEITLLA 101 KVEKCAMISS 151 LTTGSYPRLP 201 QLANLTVANG 251 DGRALVHSMQ 301 QTLMLIRERW 351 IDETDGSKPL 401 QKLQELKAIL 451 GTFQPMLYGT 501 HLPTVCSKTL 551 PTELEYKYYF 601 GTKRKLSGDQ 651 LSTMEIPHQG 701 RLQGRNNRTW 751 KVVEMFLNDW 801 GYGSTKGSSI 851 KTPSVVQLLQ 901 PTHIRLAFRN 951 TFLNMFVDSN 1001 103 SI

11 QLVPAGGPTS 61 ELLPRKTDME 111 FLDQQAFLFV 161 TCIRDKIIPP 211 RVKFRVEGEF 261 VSFIHELVQS 311 GDLVQVERYI 361 QISHEPLLPA 411 KNYNPSDNSF 461 DQSTLDEMEK 511 HLSNAASHPA 561 LSVTMLEGDE 611 GAIEPKKPKR 661 VQVEGDGCSH 711 VAELVFANCP 761 CSIAQLYECV 811 TIQWNSVTQK 861 VLFDTQGPLN 911 MYCIDIYCRS 961 QDARRRSVNE 1011

1

21 ALQPPPPGAP 71 RKIEIVQFAS 121 DTADRLASLA 171 DPITKAEKQA 221 EATLTVMGDD 271 RLFADEKPLQ 321 PAKCLTLAVW 371 CDSKLMERAM 421 IETALPTLVI 471 SINDDMKRII 521 GSLSKHRLFI 571 GPPSAQLLQQ 621 AGEMCAFNKV 671 AIRILKIPPS 721 LTSTSSKEQA 771 LDFARSLGDM 821 FHISLGTVGP 871 AINKLPTVPM 921 RGVVAIRDGA 971 DDNPPSPVGV 1021

31 SGTPATHGVR 81 RTRQLFVRLL 131 RDALVHARLP 181 TLSQLNQILR 231 PDIPWRLLKL 281 DMYNCLHSFC 331 NQQVLGRKTG 381 KIDHLSVEKL 431 PILEPCGRSE 481 PWLQQLKFWL 531 RLTRLPQYYI 581 FKPNLEELVL 631 LAHLVAMCDT 681 KGVSEETRRV 731 STRHVYLTYE 781 PSYLSLFSEI 831 NSGCSNCHNI 881 LGLTQRTNTA 931 YSLFDNTKIV 981 DVMDALMSQL 1031


41 LSVLIEFLLQ 91 ALVKWASNAG 141 SFAIPFAIDV 191 HRLVTTDLPP 241 EILVEDKETG 291 LSLQLEVLHS 341 TASVHKVHIK 391 LIDSVHARSH 441 CLHIFVDLHS 491 GEQRCRQSVK 541 VAEMFDVPGC 591 DATPGRGAKS 641 NMPFIGLRCE 691 LERSLLDCTF 741 NPLSEPVGGR 791 RLYNYRKLVL 841 ILHQLQEMFN 891 YQCFSILPQS 941 EGFYPAPGLK 991 QPPPGQPQPF 1041

Figure S2

GKQAGGTGVY 1051 PSPASFGPTP 1101 PGSPQVSGPS 1151 PPRKLPQRSW 1201 FLGSVIMRRH 1251 QTLQLKVTPD 1301 PTHILRDCVR 1351 LKSKMLFFLQ 1401 AAALMVSSIL

PITSPPTSYH 1061 SPSSLGISMG 1111 PAARMPGMSP 1161 AASIPTILTH 1211 LQRIIQQEPN 1261 NTGPWSQEEL 1311 IMKLELFPDQ 1361 LTQRLPVPQE 1411 KRFNEMHPPR

TGVTPSPSMM 1071 QTSNFASPHG 1121 ANPSLHSPIP 1171 SALHVLLLPS 1221 LQIVNSNEPG 1271 QVLEKFFETR 1321 ATQLKWNVQF 1371 PISIIVPIVY 1421 QSECTIFASV

PTQSPGTIHA 1081 TLDPSSPYAL 1131 DASHSPRAGT 1181 PTPCLVPGLA 1231 VIMFKTDVLK 1281 VAGPPFKYNT 1331 CLTIPPSAPP 1381 DMATGLTQQA 1431 HELMANLTLP


1

2

3

4

Positive selection

10 SI

5

6

7

Purifying selection


ASSPSGALRA 1091 MSPGQRSSNW 1141 SSQAMPTNMP 1191 GSYLCSPLER 1241 CRVALNPKTY 1291 LNAFTKLLGA 1341 IAPPGTIAVV 1391 DIPRQPSSSG 1441 PGGRP

Figure S2

Gene: 1 MDIAYVCEWE 51 MIHIIDSEHP 101 TEHLVNSWES 151 RVKFSPSLTL 201 GRVALADIAF 251 PSLFMRCTTD 301 LRKEGLPVNN 351 ISISNTDLKV 401 SNPQRVGEEP 451 SPSMGQMLDI 501 HEEYMRQNQA 551 STLKSLLRPH 601 ASTLQSLQQL 651 MMVVIRIWGL 701 EPDEPLIDEC 751 LPGLNSGTQV 801 RSPNKTTAVK

11 KRPKSNHCPS 61 WDVYSINSGH 111 TLGSAVEGDP 161 FGGKPMEGWM 211 TGGGNIVVAA 261 PARKDKYPAV 311 IFQHRSPVVG 361 ASDTKFCPGL 411 ALKRQRGGGP 461 NTLLRHLLFL 511 LQQVLSTRVV 561 LLNTPDKSPG 611 IQWVGDFVLY 661 LKPGCLPIYT 711 CLLPSQLLVP 761 EIFTRTPGSQ 811 QWEQRWIKNC

1

21 IPLVCAWSCR 71 TEVISCLEWD 121 IVALSWLHNG 171 AVTVSGLVTV 221 TDGSSSAPVQ 271 THLKFLTREN 321 EKQPMILKWR 371 GLALAFHDGS 421 TTHFKALQFS 471 LEYCMVTGYD 521 AMKASLCKLS 571 DRLAEICAKN 621 LLANLPNQGS 671 ATSDNQDSMF 721 AMDWLPVSDG 771 RMDNLRCLHM 821 LCGGLWRRIP

31 NLLAFTTDLK 81 QSGSRLLSAD 131 VKLALHVEKS 181 SLLKPNGALL 231 FYKVCVSVVN 281 SEQVLLCASS 331 ILSATNDLDR 381 IHILHRLSLH 431 CTSLALVGVD 481 WWDVLLHVQP 531 SATAPRACDF 581 TDTDIDKVMI 631 IVRPGFGFLR 681 LLFRLLTKLW 731 IICKLQGKHP 781 GVCPTEDSKA 831 TTIS


1

2

3

4

Positive selection

10 SI

5

6

7

Purifying selection


41 NEEEEKDLTH 91 GDGQIKCWAM 141 GSTNFGEKFS 191 TASESLCRLR 241 EKCRIDTELL 291 QLGSIVECWS 341 VSAVALPKLP 391 TMGVFYGSSS 441 NHGKLHMLRV 491 NMVHNLVEKL 541 HAKLLLIAIS 591 NLKTEEFVLD 641 DGASLGLLRE 691 LCSRDESHPQ 741 LRLQFGKPYS 791 CTRCGCVTML

Figure S2

Gene: 1 MSGGPAVRVS 51 QGSDSEDEGG 101 LTEMCVLYDV 151 AQLLLKGAEK 201 LSYKSAGSLF 251 IKVSIQKQAP 301 FAQLSREAVQ 351 SPEKSKPDDH 401 AGPMAFDKAE 451 PQIQAHWSNI 501 DGRVITLSHQ 551 GSVESIGNAS 601 DVIQDNKWNH

11 IESACEKQVQ 61 EGESRDQEWG 111 LSVVKEKKYM 161 LSKSVAENQE 211 PHHGTFEVIK 261 DIGDLGTVSL 311 IKSQIPHIVV 361 LYVLEHNLHQ 411 IASLQQNEGL 461 NDVYESSVKV 511 EQELQDFLLS 561 AITVASPNGE 611 LRGPSKEVHW

1

21 EVSLDGIETY 71 KQEAEEDEAT 121 TLDPVSHDVT 171 NRRQRDFNSE 221 NTDIDLDKKI 271 FRRQPKAKSG 321 KNQIISQPFP 371 LMREFHKQTL 421 LEKIIKQAKH 471 LITSQGYEQI 521 QMSQHQVHAV 571 FAISVRNGPE 621 NKMEGRNFVY

31 VQPLSMSQNL 81 VKFQPSLWPW 131 AGKTPQVLQL 181 LLRLRSQWKL 231 PDDYCPLDVQ 281 SQPWHAKLEA 331 GLQLSISLCH 381 SSAVMPHPAS 431 IFLRRRTART 481 CKSIQLQLNI 531 QQLAKVMGWH 581 SGCKVIVQFP 631 KMELLMAALT


1

2

3

4

Positive selection

10 SI

5

6

7

Purifying selection


41 AKLAQRIDFG 91 DSVRNNLRSA 141 IGKKKSLATA 191 RKVGDKILGD 241 IPSDLEGSAY 291 AQNVLLCKEI 341 STGEKKNQKA 391 APFGHKRLRL 441 IDSLASRIED 491 GVEQIRVVHR 541 VLSFSNHVGL 591 RSQCKDLPKS 641 PCP

Figure S2

Gene:

1 MKVVNLKQAI 51 MIGLSPNPLI 101 MDMFSHQLSC 151 EASLRACVDR 201 SLTNQVLRSK 251 NLTGETQPLV 301 WTAFTFLKIP 351 CNCDCIELLL 401 PNPGLILRAE 451 AAATGKLKSF 501 QTYGSEVILS 551 ENLVALLNNS 601 KITDNIKGKV 651 SAENTLQFYN 701 LAPREPIRAA 751 ELLRGTRQEW 801 LADPPGKALA 851 DDTQPSKLMR 901 VLANLFLLVS 951 TMVSELVKLT

10 SI

11 LQAWKERWSD 61 LSYLKYAISS 111 HGKAEECIGL 161 LEGLLRGTKN 211 LEECLSLVKS 261 EQLMMIKRMQ 311 QVLLRLKKYP 361 QECRKLGLLS 411 PTVTNILKTV 461 ARKFIKLNEF 511 DPSPSGETPF 561 SEMKLVQMKW 611 CSMAICAVAW 661 ERVVIMSSIL 711 LSHQFSEVLQ 761 VMCAVELLYS 811 KLAVWCALSS 861 LLSSNEDDPV 911 SILSSKTAGP 961 ALAKPKVVLA

21 FQWAINIKKN 71 QMVSYSSILT 121 CRSLLAALVW 171 RALIHIARLE 221 IPLMLVVQAE 271 RIPSPLFVLE 321 QGEKDFMEDV 371 EANTSNLSTK 421 DADHSKSPEG 471 PKHISGEGSK 521 FETWLQTCMP 571 HEICLSTPAA 621 LVAHVRMLGL 671 EHMCADVFQQ 721 RGWVDSQALH 771 IFCLDMQQIT 821 YSTHHKGQAS 871 ILSSPGDRSM 921 HTQFVQSFME 971 ITDLSLPLGR

31 FPKGATWDYL 81 AVSKFDDFSR 131 LLQGCAWYSA 181 EQASWTNVEQ 231 PPQRTSFPSV 281 IWKACFTGLI 331 NIAFEYLLKL 381 RAVDREHAPR 431 LLGVLGHMLS 481 PASVRALLFD 531 EDGKILNPDH 581 ILEVLNAWEN 631 DEREKPQTMI 681 TGVVLRPPME 731 LFESLLHMGG 781 LTLLGQILPS 831 ARQRKRQRED 881 SSSLSASQLH 931 ECVECLEQGS 981 RVAAKAIAAL


41 NLAEALLEQA 91 ELCVKSLLEI 141 RLREQGEQAG 191 AVIRVTENLN 241 HTLVMLEGTM 291 ESPEGTEELK 341 TPLLDKADQR 391 LKTAENANIQ 441 GKSLDLLLAA 491 ISFLMLCHVV 541 PCFRPEPGKV 591 GVLTVESVQQ 641 RQLMTPLYGH 691 GLEPVPYRNL 741 VFWFTNNLVK 791 LLTDSARWHS 841 IEDYNSLFPL 891 TVNMRDPLNR 941 RGSILQFMPF

Figure S2 Legend: The selection scale:

1

2

3

4

Positive selection

10 SI

5

6

7

Purifying selection


Figure S2

Gene: 1 MATPPVAGAG 51 FQLLRNMQLP 101 NCAGLDPVPA 151 QKNQQLKQIM

11 MPAGAFGGQQ 61 NGVTYHASTH 111 EQLIPYVEDD 161 DQLRNLIWEI

21 AQAAREVNTA 71 QDRLGKLQEH 121 GSKHDDRSTN 171 NSMLAVRN

31 SLCRIGQETV 81 LRQLSVLFRK 131 LARYATEERR


1

2

3

4

Positive selection

10 SI

5

6

7

Purifying selection


41 QDIVFRTMEI 91 LRLVYDKCNE 141 EVLEVNQKLK

Figure S2

Gene: c a1

1 MSGLGESALD 51 SANMGDIDSL 101 KSDISSSSQG 151 YPQEELMSSS 201 NCRMLKRPPD 251 IACRLPRPQL 301 IYAFFQPQGK 351 LCYPPNQDMQ 401 SPAVQPSMEL 451 LNSPSPLGSP 501 PAGAPSGSGN 551 PLAKPAEGLP 601 PCPASHSSLT 651 EPQDHQLLRF 701 PNDRPRNQVA 751 TYHLFQPSLQ 801 VKLPEEQGDS 851 CSPSTPSQGQ 901 PPPMAEPMPF 951 KALLDQLVSF 1001 110 SI

11 PTNLDSLKRK 61 SVKPDKCHIL 111 MIEKEALCPL 161 VYSILHVGDH 211 EVDSENQEAR 261 PVSTESFITR 311 EPSYAKQLLQ 361 PFIMGIHTID 411 GQTAGMGVHL 461 LGTTPTSFMS 511 LSRQQSGCHG 561 ESREDHTKTP 611 ERHKILHRLL 661 LLDTDDKDLG 711 LFPSMPELKH 761 LNPATLLYYF 811 PQPGESSLPR 861 GDHFLSPKGS 911 EGNMGSVNDS 961 LSGTDESELA 1011

21 GSPCDTSGQS 71 KSTVDQIQQI 121 LLEALDGFFF 171 NEFVRNLLPK 221 QQYEIMQCFT 271 QDPTGKIISI 321 EVISHGTAIS 371 REHNTASSQE 421 NNGNSSGTGP 471 PRPPRGSPGL 521 ECAGTPLSFS 571 QQLSNAKLGQ 621 QDNSPTEPTE 671 GLPPSSALSL 721 HSGFLRLEKK 771 FTYLRIREVL 821 GVSVKQEPSS 871 SPFRESGHVN 921 ALTVPPEQCI 971 ALDRALGIDK 1021

31 VEKRRRELEC 81 KRREQEKAAA 131 VVNREGRIVF 181 SLVNGVPWPQ 231 VSQPRAMHEE 281 ETSALRATGR 331 PVYRFTLNDG 381 NTNTGPLSTH 431 ATPTSHPPGY 481 GGSPRVSGNP 531 TPSPVPQRQT 581 LLDGCGGRPS 631 GGRKDMEIKK 681 QTVRVKAGKT 731 IQSVISFKYP 781 AAADLDTVSQ 831 TPGRGFSDGP 881 TFRTDTGLPK 931 PCPLDEMLCP 981 LVQGCCLDSL 1031


41 RYIEELAELL 91 ALMSPDDEVQ 141 VSENVTNYLG 191 ESTGRNSHTF 241 GEDLQSCLIC 291 PGWEDLVRKC 341 TTLSAQTRCK 391 GSQSPAQPTR 441 LTPSRMGTQQ 491 FSPSTPSLHS 541 STPASSPVRP 591 ETDTPPSLPA 641 EPSASSPSSR 691 PEAESSASPK 741 LFVILQVSDS 791 LLHTLAGGPG 841 RLQSQSPFEF 891 MELTGSQQFH 941 PTTVEGRNDE 991 SQQFPAQAPM 1041

Figure S2

LMDPKPPGYT 1051 LARPPGLPNQ 1101 MQQPQLPSQQ 1151 GPMGVARIPK 1201 ARGPMANQGL 1251 LSPTSPLLSP 1301 SGQTPPQAFG 1351 VSSMCNDQVQ 1401 SQQKSLLQQL

SQFPPGSPQF 1061 LRLQLQQRLQ 1111 PPLNAQMLAQ 1161 GPQQQQQFTF 1211 MGNVQGQFGG 1261 QISTSQSPML 1311 QQGVYNNMSI 1361 QVQVFADVQC 1411 LTE

SSAMGRAQGL 1071 GQQQLMQQNR 1121 RQRELYSIQH 1171 PPGYSPAAGN 1221 AMNSPVQPSI 1271 QQTQPPPGYQ 1321 TVSMAGGTGG 1371 TVNLVGSDPY

GFGGPRGAFP 1081 QAQMGQFPGA 1131 RQRQLLQQKA 1181 PPNSPSPFTP 1231 FQQFGGPGMV 1281 SPDLKNWQQG 1331 VGSIPSMGPP 1381 LNQSGPLGSQ


1

2

3

4

Positive selection

111 SI

5

6

7

Purifying selection


GGIGMGPRPP 1091 VPVAMGMRPS 1141 MLMRQQGFAG 1191 MGGPPDPTLP 1241 QQGEPPFPPA 1291 SMGNNSMYNQ 1341 VGMGNSNMGS 1391 KGGAGAQTTP

Figure S2

Gene: nc a

1 MSGLGDNSLD 51 ANLSDIDNFN 101 GQGVIDKDHL 151 NTSVYNILHE 201 GHSPPEEGAG 251 RTESFITKHE 301 WSHKRHYQEA 351 FISTHLLQRE 401 RGFSMNESGH 451 QQQPPYQGSG 501 PGGMHSPMGP 551 AHKPDSSPSI 601 HHTPTESATD 651 LTSPTDDLGM 701 SSAAQPPGGV 751 TGKETSSHEA 801 HYLLNNDPKE 851 QPDELHDTLE 901 RSPAGLRSPE 951 DNQRMMGGPE 1001 112 SI

11 PLCSDRKRKL 61 VKPDKCAILK 111 GPLLLQALDG 161 EDREEFHKNL 211 SPRYETMQCF 261 LSGKLIQIDH 311 FMQGHAETPL 361 QNGYRANQGP 411 MGQMGGSMYG 461 YGLGMNSPSQ 511 GSAGGAGGGG 561 NSSQQQQQQN 611 RPDSQASLRV 661 VAGGVPPTGA 711 SSSSSSAHHA 761 GVADLGTIGT 811 PADIKPKLEE 861 TILGGFRNSS 911 LGPRGPFQRA 961 NFPGNMGMVN 1011

21 STCDTPGLGC 71 ETVRQIRQIK 121 FLFVVNRDGS 171 PKSNMNGVSW 221 ALTQPKAMME 271 SSLRSTMRPG 321 YRFSLSDGTP 371 MIQGMRPMGN 421 ATNRMMQMNP 471 GSPGMNVPQQ 521 NSNFSSSSLN 571 QQCKAGRVDS 621 TKEGSEVGTG 671 STPSTLEPKE 721 ASLQEKHKIL 771 AGTGGGGVGG 821 LEGKTQQNAC 871 SSFYQESGVG 921 VSVDGKPPVG 971 RGLGVPQRSP 1021

31 DKRRREQESK 81 EQGKASSNDD 131 IVFVSDNVTQ 181 ATEAPRQKSH 231 EGDDLQSCMI 281 WEDLLRRCIQ 331 VTAQTKSKLY 381 STPNASMNMP 431 MSQMSQMGQM 481 NLMVSPRTRG 531 ALQAISEGVG 581 PSPAGMYVPG 631 GAEPQRRLSD 681 PAGCVTSPSS 731 HKLLQNGNSP 781 SGVPDIKQEQ 831 SSSGLMPSTP 881 AGSDVANKQP 931 ANSLGRRSAP 981 MGGSGEWGIQ 1031


41 YIEELAELIS 91 DVQKADVSST 141 YLQFKQEELI 191 TFNCRMLMKY 241 CVARRITAVE 291 MFMHHSEGQP 341 RNPMTNEPQG 391 PGPGMGMGGN 441 SQMNHPGPGM 491 SPKMVPSQFS 541 NPMPSSLSSP 591 GDHHHHLHHH 641 SKGNKKLLQL 691 TGVSSSSSSS 741 DEVAKITAEA 791 PSPKKTHALL 841 ENGENKIKTE 891 ACPDDAMHGL 941 CPMLVKQESM 991 RSNASPVGTS 1041

Figure S2

SHPMVRPGMD 1051 MTPFNQQGPP 1101 EGQSDERALL 1151 FPGQDPALVM 1201 MSQQGNFPMA 1251 LGMKMDNTTA 1301 RMMMLMQQQQ 1351 NYGINQQGDP 1401 MKSWPQGGMP 1451 PGQMNMNPMA

YSSKPMMGGP 1061 NQSPSWPENV 1111 DQLDSLLNNT 1161 DQKPPMYSQG 1211 GMHPRPNMIR 1261 GNPGLRPALQ 1311 QAAAGGFSPP 1361 SFVRAAGSPP 1411 RSSSYPQQQF 1461 MGRMPMGPEQ

MVGRSNSVPG 1071 MPIEHGPQNS 1121 DVMALEEIDR 1171 YPGPPGMAMQ 1221 PRMMNALKPL 1271 APMGGQPGFL 1321 PNVTAPAGMD 1371 NSIMSARLGP 1421 PQQGNPGSYG 1471 KYC

NRSMLQQQLM 1081 QSRRQFANPL 1131 ALGIPDLVSQ 1181 PAYSSPMQGQ 1231 RQQLVQRLQG 1281 NAQMMAQRNR 1331 TPMGGPPMTQ 1381 PQNPMMQQHP 1431 NMMMNGSLPV


1

2

3

4

Positive selection

113 SI

5

6

7

Purifying selection


DMGPNDINMG 1091 DDLLVPPATS 1141 GQGVDPQSEP 1191 PPGFNPMMNQ 1241 QQFMNQSRQG 1291 EMLNHQLRRQ 1341 PGPQQFSYAA 1391 QGGPMYPTAD 1441 NGNGGHMGQM

Figure S2

Gene: c a 1 MSSAVEDRDR 51 CISRHLEVLR 101 QLENNNSNNL 151 GTIETKQLSY 201 ILKSSSGSSP 251 VEAWVLKDRV 301 KDWLVTSPTE 351 GACRGQSKAV 401 GSFLDCVCEE 451 WLHPRKKEVP 501 WLMPRRKPSL 551 DMEKWLYKAP

11 DSLRRCLQAR 61 SREVWLLEQI 111 ANQITSCLEK 161 YLISPPSKSS 211 QSGCQLSFNL 261 PPRERSVSET 311 EKEELAENKS 361 EIENLGALKC 411 NCGREALCGL 461 ASSFPSYGLT 511 PAPCTNTEED 561 IQHILPDH

21 CQLEASISGV 71 EIVQHLKEEA 121 LSSLNLKPEE 171 LDDVWLFQNC 221 DDWLYKPKEK 271 SSSTMMSIEK 321 HADDKPKTMF 371 LKHSPSPSPA 421 LFKKEGRDKN 471 LQPQEQEKTT 521 KWLLRKRAPV

31 TRAELQLRDN 81 LQQQHHQLHC 131 TPEMSFQADI 181 PLAYTQPKVE 231 SQVSCPFAQF 281 IEDADLNLSE 331 WPFSEPFRAS 381 ATSSTETVRV 431 GMPLDKNKVL 481 QEEPELKCKD 531 AEQNGPTSFS


1

2

3

4

Positive selection

11 SI

5

6

7

Purifying selection


41 SREVKAQIHS 91 LLGQLNFLIY 141 RSLRQAITSF 191 SKLWTELDNW 241 EFDKMCTKTD 291 GEEGQETEDL 341 DWLVKYDDSC 391 EQVCKANEPC 441 EESYVNDIDR 491 PFKVSFNPED 541 DLFACMTLKG

Figure S2

Gene:

1 MSASVKPLTS 51 DTRHARETGS 101 LELEKKFSHQ 151 EYGKDPFKRA 201 AV

11 FLIQDILAFK 61 HDKNTSTDLK 111 KYLSAPERAH 161 TGLPCVGTEE

1

21 EESRLSTPRY 71 AVGNGEETPQ 121 LAHSLRLTET 171 DLIRASLFAT

31 ACAKEPRERD 81 SSSSGGKQKR 131 QVKIWFQNRR 181 MYKTYHDQQP


1

2

3

4

Positive selection

11 SI

5

6

7

Purifying selection


41 KSPDSISAGR 91 SRAAFTHLQV 141 YKTKRKQLAT 191 CLYGLNVWNS

Figure S2

Gene: nrip1

1 MTHGEEPGSE 51 NNKTVGSHQL 101 LPASVVNLNG 151 QQIMQNLKQQ 201 VPYQRRNSQE 251 TSSPKPSVAC 301 QQTQDIKQSS 351 VNSSQRSLHS 401 MEEDYSVFPN 451 GRASGSGLGS 501 KVTLLQLLLG 551 TRTRNSPDAL 601 KAKSHSNENV 651 EPRTDKPVAL 701 NLLERRTVLQ 751 EPTLDIKIKT 801 EVLSAEAIPK 851 KKRKLCMGMD 901 LEADSLLQVG 951 IIQANCKING 1001 11 SI

11 MHQDSAVLTY 61 PNHSSNQEDR 111 QNRDLLTGAL 161 DNLQSDKSTQ 211 RFSDSPEASQ 261 SQLALLLSSE 311 MGQHQVSADI 361 FRDKHSFDRH 411 HSSPLRSESE 461 SSSLDKLTET 511 HKNNEKVNKN 561 CFRKLQSLPV 611 EESSFSASKL 661 LERLNAPLTK 711 LLLGATTSKE 761 EPRDEVHLSN 811 DGLLSQLLKH 861 ETLNTEPCIR 911 CPVSESLPKD 961 NIPSKSGYNH 1011

21 LEGLLMHQVS 71 SVPLGRATQH 121 DSSPKCKAES 171 VEDEALRCYG 221 SSVQPAARDS 271 AHLQQYSREQ 321 VNPLNGQNGT 371 SSRPSPNCSS 421 YSNLENSLTK 471 LISNWNPETS 521 SDNPDLQSCT 571 FSQEQDTNGS 621 LQNLAQCGLQ 671 NKTTVLEEPL 721 KASGKRKRPV 771 TNGEEKRSQV 821 PPSTYQVKNQ 871 AVSAVQRDGS 921 GKGFNVLKQL 971 DFAVLQHNSS 1021

31 GRQSAAATRR 81 LKKARLLRSS 131 TLLASLLQSF 181 SASSRLKGLL 231 ISCAARLKAV 281 ALKAQLSGRS 331 LPQTVDSSKP 381 LLLHLLNNHN 431 DNSDAESSHS 481 SHKVTEARES 531 TSKPNCLPTG 581 ASPYSLSLSP 631 KSIPSPPVET 681 VNSMKLPYVM 731 DKGDSLDKHS 781 EERLNGGNNP 831 DVCTISGKEG 881 SEPSGSRTSD 931 LLSDNCLKDI 981 PQGPVSLDFK 1031


41 SDAGHSERNQ 91 EAWNGPETQQ 141 SSRLQSVALS 191 KKNKMQNHNS 241 ASIVKNRSSP 291 ASERLAAMAT 341 SPSPIQGQSR 391 TQKYTNGNSL 441 SCSPIDLSVK 491 ENSSVIKPHH 541 RVTPSSRFEE 591 QVQAIPLDLC 641 SVSPGIRQTY 691 DPSPSVSEIE 741 DPSPGSGNSY 791 HSSNQKDIKS 841 LSLNQGPAIP 891 GRNVHNEVNR 941 SLPRSATSPS 991 PLSAASERSK 1041

Figure S2

PPGSPWGYHA 1051 TKSNPILYYM 1101 RLKHHHQLSN

ARQDSPKLNL 1061 LQKGNSHIGK 1111 EKQGNETESF

IPVKRELEGP IQWVISGEEK QDPSIDSPRL 1071 1081 1091 LRKAEAPECE MQVKVKEEPM SELDAYSHRL 1121 NRTVEKC


1

2

3

4

Positive selection

11 SI

5

6

7

Purifying selection


Figure S2

Gene:

1 MVMSLRVSEL 51 LYRRRFPTKM 101 LLGPKHELDL 151 RFQETCFAFA 201 DHFPPNLCVK 251 PNTIVVSWTA 301 KEKLTADPDS 351 IQMNEKKPTW 401 WAPMRSKKEV 451 SSDEEEDEEP 501 TNYIPPPPPL 551 AAASASDEHD 601 SSSSSLVSSS

11 QVLLGYAGRN 61 VTPAELSLPS 111 PHLPSALHPV 161 LTPQQVQQIS 211 VNGKPCNLPG 261 EIGRSYSMAV 311 EIATTSLRVS 361 VCPVCDKKAP 411 QQVNSYNGVE 461 PPKRTCPSLS 511 IQDYRHSYHT 561 MLHPSLNRFL 611 SLRESHGHPG

a 1

21 KHGRKHELLT 71 VHSTTAPLPA 121 HPDVKLQKLP 171 SSIFLSQQIR 221 YLPPTKNGVE 271 YLVKQQSSSV 321 LLCPLGKMRL 371 YEHLIIDGLF 421 GACRTAIPEH 471 PASPPVNKGV 521 LPYELQGLDF 571 PYNSSQMYLE 621 PTRATAEAAA

31 KALHLLKAGC 81 GLPQLSFDGH 131 FYDMLDELIK 181 HITFQDTLKF 231 PKRPSRPINI 281 LLQRLRSKGI 331 MIPCRALTCS 381 MEILNSCVDC 431 RHSSSSNSKK 481 LNLHHQASPV 531 FPFLQGDNQH 581 QPGTPVSSAL 631 AIYGSMPDVI


1

2

3

4

Positive selection

11 SI

5

6

7

Purifying selection


41 SPAVQMKIKE 91 AASSPLLPVS 141 PTSLASDNSQ 191 CLSETSCPQE 241 TSLVRLSTTV 291 RNPDHSRALI 341 HLQCFDATLY 391 DEIQFKEDGS 441 VEVIDLTLDS 491 ARAPSMPPVD 541 YSTNLLVAAA 591 VPANGGGSSS 641 SLD

Figure S2

Gene: 1 MTLTQPAPPI 51 IFALTPQQVR 101 LCIKVNGKPF 151 TWAPEIGKTY 201 DPDSEIATTS 251 KPTWICPVCD 301 KKETLKVSAQ 351 KRCLYMSKPE 401 HSTLSTISAD 451 SSHYESSSHS

11 PPVHPDVQLK 61 EVCISRDFLP 111 PLPGYPPPPK 161 SMSVYLVRQL 211 LRVSLMCPLG 261 KKAAYESLII 311 CSTKIETSDP 361 EVHGKGVLTY 411 MQISETDAQW 461 SGSARNETGV

a

21 SLPFYDVLDV 71 GGRRDYMVQI 121 NGVEQKRQGR 171 TSSLLLQRLK 221 KMRLTVPCRA 271 DGLFMEILND 321 SSLKKADIID 371 QPSTVRVPNV 421 DSGRYRTPMF 471 ITGGGGTIIP

31 LIKPSSLGAS 81 QLRFCLAETS 131 PLNITSSVRL 181 MKGIRNPDHS 231 VTCSHLQCFD 281 CTDVDEIKFQ 331 LTIESSSEGE 381 QTVETSYITS 431 LDNLPSTLQQ 481 DIISLD


1

2

3

4

Positive selection

11 SI

5

6

7

Purifying selection


41 SIQRFQEKYF 91 CPQEDNYPNS 141 SSAVPNQISV 191 RALIKEKLTA 241 AALYLQMNEK 291 EDGSWCPMRP 341 EEEEEIPPLK 391 PLADYAVPFH 441 QATSGGLIST

Figure S2

Gene: 1 MSAEGYQYRA 51 DEIGWLHGFN 101 PTKADSDSEQ 151 GSCSGLEIRQ 201 SEMVHVAQEV 251 TGKNLLSARV 301 AAPALPPKPP 351 GTFLVRDAST 401 ELINHYRHES 451 HQQYQEKNKE 501 RYSKEYIEKF 551 AADYREIDKR 601 ETTEDQYSMV 651 SSKQGCFACS 701 TSLVQHNDSL

11 LYDYKKEREE 61 ETTQEKGDFP 111 ALLDLTEQFS 161 CFESDPCAVD 211 HNPEECALLL 261 LGDVFSPLVF 311 KPAPVTNNGM 361 KMHGDYTLTL 411 LAQYNPKLDV 461 YDRLYEEYTR 511 RREGNEKEIQ 561 MNSIKPDLIQ 611 EDDEDLPHHD 661 VVVDGEVKHC 711 NVTLAYPVYA

r1

21 DIDLHLGDIL 71 GTYVEFIGKK 121 PPELAPPILV 171 LDQFDLQTLC 221 RRIVQSPNVP 271 RHQAASCDAS 321 NNNMSLQDAE 371 RKGGNNKLIK 421 KLLYPVSKHQ 471 TSQEIQMKRT 521 RIMVNYEKLK 571 LRKTRDQYLM 621 ERSWKLGNIN 671 VINKTPTGYG 721 HQRR

31 IVSKGALLAL 81 RISPPTPKPR 131 KLVEAIERKG 181 DGLRRYLQDL 231 HQYWLTLQYL 281 PEYHIRIIEV 331 WYWGDISREE 381 IFHRDGKYGF 431 QDQVVKEDNV 481 AIEAFNETIK 531 SRISEIVDSK 581 WLTQKGVRQK 631 RVQAEALLRG 681 FAEPYNLYNS


1

2

3

4

Positive selection

120 SI

5

6

7

Purifying selection


41 GYGDGFEEKP 91 PQRPLPVAPG 141 LDCPTLYRNF 191 PHPVVPVSVY 241 IKHFCRVCQN 291 FITSEWNESQ 341 VNEKLRDTAD 391 SDPLTFNSVV 441 EAVGKKLHEY 491 IFEEQCQTQE 541 RRLEEDLKKQ 591 KLNEWLGIKN 641 KRDGTFLVRD 691 LKELVLHYQH

Figure S2

Gene: 1 MSAEGFQYRA 51 GELGWMVGVN 101 AEPPPVRQAL 151 MRDTPDGTFL 201 TFLSVVELIS 251 EQLRVYHEQY 301 QCETQERYSK 351 QDLKKQATDN 401 WLGITNEAED 451 FLIRDSQSQK 501 VLHYKHTSLV

11 LYVYNKDWDE 61 ERTKQRGDFP 111 PPKPPKTKAL 161 VRDASSKVQG 211 HYRHESLAQY 261 QEKSREYDVL 311 EYIEKFRREG 361 REIDKRMNSL 411 LYSLMDEEDD 461 GSYACSVVVD 511 QHNDSLNVTL

r

21 DVDLQPGDLL 71 GTYVQYVGPV 121 TNLVANGNSS 171 EYTLTLRKGG 221 NAKLDTRLLY 271 YEEYTRTSQE 321 NDKEIQRIQS 371 KPDLMQLRKI 421 LPHHDERMWY 471 GDIKHCVIYK 521 AWPVLSPQPR

31 TVNKASLLAL 81 KMSLPLNQPR 131 LLADAEWYWG 181 NNKLIKIFHR 231 PVSKYQQEQV 281 LQMKRTAIEA 331 NSEKLKSRVT 381 RDQYLVWLTQ 431 VGDVKRVQAE 481 TVTGYGFAEP


1

2

3

4

Positive selection

121

5

6

7

Purifying selection


41 GFKEGDEERP 91 FQRPLPAAPR 141 DISREEVNEK 191 GGMYGFSEPL 241 VKEDSIEAVG 291 FNETIKIFEE 341 EIHDSKRKLE 391 KGTRQRRINE 441 DLLRGKRDGT 491 YNLYGSLKEL

Figure S2

Gene:

1 MFDTKGIPFV 51 HSSTVTSTTL 101 KAVGTFVFGA 151 ENFTCTGDKT 201 LLRPTIQFFL 251 SDFFKKPVQP

11 LLDLACLVLA 61 YTVGFTLPIC 111 AMSQSLTDIA 161 MVNEGSSSFK 211 IAASVYTGLS 261 QKPVEIPHTT

a

21 GLPLAAFNLA 71 SMVVGECLSV 121 KYSIGRLRPH 171 QGHNIIKLIR 221 RVSDYKHHWS 271 LQETPTNGNH

a

31 KIKPYRRGFF 81 YLNRLKSKSS 131 FLDVCKPDWR 181 LLKEILALYL 231 DVLTGLIQGA 281 YDSPN


1

2

3

4

Positive selection

122

5

6

7

Purifying selection


41 CNDESIGYPF 91 FSNSYVACVY 141 LINCSAGAYI 191 QARMQAEWAR 241 VMAVLVVFFV

Figure S2

Gene: 1 MGLTNGTTDT 51 LVITCLLNHY 101 EVYTPRAPDR 151 YQGPCTLQLR 201 PAYSEVIGHY 251 TRMFSPKPGH

11 LANVSCTCNC 61 RLSARSLMSR 111 VPSFLQRERV 161 DREQQLELNR 211 YHPTTLPSPC 261 RKRPEELLPN

a1

21 QRSTSFQSMA 71 HTHERRRHLP 121 SRFQPTFPFL 171 ESVRPPPNRT 221 RFRAPSAGTS 271 QLTWKILGSL

31 ISQLEFVQIL 81 LPSEGSLWSS 131 PPVIELPPTI 181 VYDSALTHTG 231 PTAVVLASAP 281 APGRCSMLSQ


1

2

3

4

Positive selection

123

5

6

7

Purifying selection


41 VIVVVMMMMV 91 DGPGSSSAMS 141 ALSDGEEPPP 191 ISGGRLQGPP 241 PLSLPNIHSS 291 WERY

Figure S2

Gene: 1 MAWDRCNQDS 51 GGLKWYSDQS 101 EDGLPSFDAL 151 NSQLSYNQYT 201 KPTRRPCAEL 251 ASSSSSSSKK 301 SIERTLSVEL 351 KRPHYSDSAV 401 GDHDYCQFVS 451 PDQDLWCNRE 501 NEDEKAGPQQ 551 EGTHLDLLFG 601 RSRSSSCHRR 651 PPIHSRSQSR 701 ERQRQKAIEE 751 NFGFITYRYT 801 SHSDDFDPSS

11 VWRELECAAL 61 EIISSQYGSE 111 AEGDVTNTSD 161 GGKAQNEAPS 211 LKYLTASDET 261 KPVHPSQQQL 311 SGTAGLTPPT 361 CPSIKKGPEQ 411 TKRDISLAYS 461 GKQLQTYQNR 511 RDESDSEYYY 561 GSPSCSPSSC 611 RSYSRSPYSR 661 SPFSRRPRYD 711 RRVVYVGRLR 761 CDAFAALENG 811 TKSKYDSMDF

ar c1a

21 VGEDQPLCSD 71 PSNLFEKIDE 121 QSCPSSPDGS 171 NQRIRPTPAV 221 IQTKACEQKS 271 HHQRAKPTTL 321 TPPHKATQEN 371 TELYAQLSKV 421 VESQDGRQLE 471 QQANSRKPLR 521 KLTDYVHPGL 571 SPSRSSVSPP 621 SRSRSPYSRS 671 SYEEYQHERL 721 PDITRTELKR 771 HTLRRSNEPQ 821 DSLLKEAQRS

31 LPELDLSELD 81 ENEANLLAVL 131 PPTPEAEEPS 181 VKTENPSWNN 231 GGGSSSKVKS 281 PLPLTPESPN 331 PFKPSVKPKL 381 SALPAGQEDR 431 CWDLVLSPSS 481 DQEIRAELNK 531 PMEGVFDDSE 581 KSLFSSQRCH 631 SSRSHHCVDS 681 KREEYRRDYE 731 RFEVFGEIEE 781 FELCFGGRKQ 831 LRR


1

2

3

4

Positive selection

12

5

6

7

Purifying selection


41 VSDLDADSFL 91 TETLDSLPVD 141 LLKKLLLAPA 191 KQRVPCQQQQ 241 GGASSSSSSV 291 DQKGSPFENK 341 SSCSSSAQAS 391 KSKRSTLRLF 441 LAVQQQNYSS 491 HFGNPKQAIY 541 DENEKFLYPW 591 WSRSASHSRS 641 SNTRPRSRRS 691 KREFERAEQR 741 CAVNLRDDGD 791 FCKSNYTDLD

Figure S2

Gene: 1 MFQWRRSCCL 51 HKNHYKIYNL 101 WLSEDDNHVA 151 RDKKGVTIPS 201 CRDTAVKNKT 251 YMFFEFPQPL 301 EKVENGSLVG 351 FSPNFKVKLY 401 PENEPFDEEQ

11 AHLVISYIYP 61 CAERHYDAAK 111 AIHCKAGKGR 161 QRRYVYYYSY 211 EQIPHGFRKG 261 PVCGDIKVEF 311 VKELDGIQST 361 FTKTVEEPSN 411 HTQITKV

21 NIIAMGFPAE 71 FNCRVAQYPF 121 TGVMICAYLL 171 LLKNQLEYKP 221 NWHWDPQFVV 271 FHKQNKMMKK 321 ERGDNDKDYL 371 SEASTSTSVT

31 RLEGVYRNNI 81 EDHNPPQLEL 131 HRGKFLKAQE 181 VALLFHKMVF 231 YQLKVKIHTS 281 DKMFHFWINT 331 ILTLTKNDLD 381 PDVSDNEPDH


1

2

3

4

Positive selection

12

5

6

7

Purifying selection


41 DDVVRFLDSK 91 IKPFCEDLDQ 141 ALDFYGEVRT 191 ETVPMFSGGT 241 NPAHTRREDK 291 FFIPGPEENL 341 KANKDKANKN 391 YRYSDTTDSD

Figure S2

Gene: ptk2a

1 MAAAYLDPNL 51 TWASNIRHGD 101 DMGVSHVREK 151 VRNDYMLEIA 201 VGLRRFFPKS 251 YRFDKECFKC 301 TIQYSSSDDK 351 VNGASQSFII 401 IIDEEDTYTM 451 SVAIKTCKNC 501 ELCTLGEVRT 551 VVVAVAENNS 601 PADRSSERDT 651 NCPPTLYSLM 701 RRQVTVSWDS 751 GYPGSHGMSS 801 DLRGMGQGLP 851 DREDCSLQGP 901 DSYNEGVKIQ 951 PPEEYVPMVK 1001 12

11 NHALGSGAKS 61 ATDVRGIIQK 111 YELNHPQEEW 161 DQVDQEIALK 211 LLDSVKAKTL 261 ALGSSWVISV 311 DRKGMLQLNV 361 RPQKAEGERA 411 PSTRDYEIQR 461 TSDSVREKFL 511 QFMGIVGKES 561 RTSTSLSLLL 611 VFAGVCMWEI 661 TKCWAYDPSK 711 GGSDEAPPKP 761 MPSAVYPPQA 811 THLMEERLMM 861 MGNQHIYQPV 911 PQEISPPPTA 961 EVGLALRTLL 1011

21 RLSMGMERSP 71 IVDIHKVKCV 121 RYELRIRYLP 171 LGCLEIRRFF 221 RKLIQQTFKQ 271 ELAIGPEEGI 321 AGAPEPLTVT 371 LPSIPKLANN 421 ERIELGRCIG 471 QEALTMRQFD 521 MSLSVTLMYV 571 QHLWENKYIH 621 LMYGVKPFQG 671 RPRFTELKVQ 721 SRPGYPSPRS 771 SVLDPHDSWN 821 QQQQMEEDQR 871 GKPEHVAPPK 921 NLDRSNDKVY 971 ATVDETIPVL 1021

31 GALDRVLKVF 81 SCYGLRLSHL 131 KGFLNQFTDD 181 REMRGNALDK 231 FANLNDEQSI 281 SYLTDKGSTP 331 TPSLTIAENM 381 EKQGVRTRTV 431 EGQFGDVHQG 481 HPHIVKLIGV 531 VHNLLKPLNT 581 NNTHLNTEEL 631 VKNNDVIGRI 681 LSTILEEEKA 731 SEGFYPSPQH 781 HHRPQDIPMW 831 WLEQEERFLK 881 KPPRPGAPSH 931 ENVTGLVKAV 981 PASTHREIEM 1031


41 HYFESNSEPS 91 QSEEIHWLHP 141 KPTLNYFYQQ 191 KSNYELLEKD 241 LKFFEILSPV 291 THLANFNQVQ 341 ADLIDGYCRL 391 SVSETDDYAE 441 VYMSPENPSL 491 ITENPVWIIM 541 DSSYCQSKLI 591 IEQLVLPVLW 641 ENGERLAMPP 691 QQEERIRMEM 741 AVQHNHYQVS 791 SPNMEEGGAL 841 PDPRNSRGSI 891 LGSLASLNPV 941 IEMSSKIQPA 991 AQKLLNSDLA 1041

Figure S2

ELINKMKLAQ QYVMTSLQQE YKKQMLTAAH ALAVDAKNLL DVIDQARLKM 1051 IGQPRPH


1

2

3

4

Positive selection

12

5

6

7

Purifying selection


Figure S2

Gene: ptk2b

1 MSGDSRTLSW 51 KNFKLVKCDS 101 WLHPDLTVGD 151 FYQQVRCDYM 201 ELLEKDVGLD 251 ETLSSVSSFE 301 FKQIRSIKCS 351 CRLENGANTS 401 YAEIPDERPK 451 VAVKTCKDCS 501 YQYGELGNYL 551 VLVAAPECVK 601 SSDVWMFAVC 651 YTLMTRCWTY 701 FDPIITVSEP 751 YQTPVDSNNR 801 ETLKRQKQEM 851 PEKPPRLTAQ 901 YVNVVKSVGL 951 KMKLAQQNAI 1001 12

11 TLGSTGKGEP 61 SWEVKEIINS 111 VVQKYEQRHC 161 QRCANKVSDG 211 LFFPKELMDS 261 EEVYPCELVQ 311 LQDNDRGQLH 361 VIVRPRKDKD 411 SVIKFGISRD 461 PDVKEKFMSE 511 TDNKHNLTTA 561 LGDFGLSRYI 611 MWEIMSMGQQ 661 DPQERPKFTE 711 PPKPSRMKSS 761 LLLPRQVPRR 811 IEDNKWLEKE 861 QPAPTAEMDR 911 TLRDLIRSVD 961 TSLSEECKRQ

21 SGLSERTNDT 71 ILSSGRLGPN 121 EAEWRYDLRI 171 MALQLGCLEI 221 MKPKHLRKMI 271 GWSIAVDLVI 321 LEITGAKQLL 371 FRNSLPAVPT 421 DIVLGRILGE 471 AVIMKKLDHP 521 TLILYSLQIC 571 EDEEYYKASV 621 PFFWLENKDV 671 LVCKLSDMFK 721 RFGSTLNVGL 771 RSMGEGDFIV 821 EKLLDPMIQE 871 SEDKVYHFVM 921 EVLPTLHASK 971 MLAAAHTLAM

31 LSVGDKIIKV 81 ITFSGCYGLL 131 RYIPNNFIEK 181 SNRRFYKDMN 231 QQTFQQYATL 281 GPKGIRQRSN 331 SINTSNLAMA 381 ADHKNMGSNT 431 GFFGEVHEGV 481 HIVRLIGIIE 531 KALAYLEGVN 581 TRLPIKWMAP 631 INQLEQGVRL 681 MEKEQETLQQ 731 QIQLPESLCA 781 EPVSKEDAQR 831 GSKTSEVPEK 881 ELVKVVVQLK 931 RTEIEGTQKL 981 DSKNLLDAVD


41 CFTSNSFNLG 91 LKHLKSDEIY 141 FKEDRTTLLY 191 AKGLEKKSNF 241 KEDECIAKFF 291 KEAVAICLAE 341 ENMADLIDGY 391 TVRESVGSDI 441 YKDKKGERIS 491 EDPVWIVMEL 541 MVHRDIAVRN 591 ESINFRRFTC 641 PKPDICPPTL 691 SKNRSRATKF 741 SSPAIASPPD 791 LWEIEKARMQ 841 ESGYAQFTGP 891 NDVNVLPASE 941 LNKDMAELIS 991 QARVRANTAK

Figure S2

PSAS


1

2

3

4

Positive selection

12

5

6

7

Purifying selection


Figure S2

Gene: rac1

1 11 21 31 41 MQAIKCVVVG DGAVGKTCLL ISYTTNAFPG EYIPTVFDNY SANVMVDGKP 51 61 71 81 91 VNLGLWDTAG QEDYDRLRPL SYPQTDVFLI CFSLVSPASF ENVRAKWYPE 101 111 121 131 141 VRHHCPNTPI ILVGTKLDLR DDKDTIEKLK EKKLTPITYP QGLAMAKEIG 151 161 171 181 191 AVKYLECSAL TQRGLKTVFD EAIRAVLCPP PVKKRRRKCR LF


1

2

3

4

Positive selection

130

5

6

7

Purifying selection


Figure S2

Gene: ra 1 1 MEHIQGAWKT 51 SKASSTIRVY 101 HPGQRSRKSR 151 CDICQKFLLN 201 SGAPSLPPLT 251 RQRSTSTPNV 301 VPAHRERAPA 351 TVYKGKWHGD 401 MTKDNLAIVT 451 KHIIHRDMKS 501 MAPEVIRMQD 551 GRGYLSPDLS 601 SLPKINRSAS

11 ISNGFGLKES 61 LPNKQRTVVN 111 MDWNTDSTSL 161 GFRCQTCGYK 211 SRRMRDSLSR 261 HMVSTTMPVD 311 SNTQEKNKIR 361 VAVKILKVTD 411 QWCEGSSLYK 461 NNIFLHEGLT 511 NNPYSFQSDV 561 KLYKSCPKAM 611 EPSLHRASHT

21 VFDGQCMSPT 71 VRPGVTLHNC 121 IGEELLVEVL 171 FHEHCSTKVP 221 FPPSSQHRHS 271 SSIIEDAIRS 321 PRDKRDSSYY 371 PTPEQFQAFR 421 HLHVQETNFQ 471 VKIGDFGLAT 521 YSYGIVLFEL 571 KRLVADCIKK 621 EDINSCTLTS

31 IVQGFPYQRR 81 LIKALKVRGL 131 DHVPLTTHNF 181 TMCVDWSNIR 231 TPHAFNYITP 281 HESGSPTSQS 331 WEIEANEVML 381 NEVAVLRKTR 431 MFRLIDIARQ 481 VKARWSGSHQ 531 MTGELPYSHI 581 SKDERPLFPQ 631 MKLPVF


1

2

3

4

Positive selection

131

5

6

7

Purifying selection


41 SSDDGKIPDP 91 QPECCAVFRL 141 VRKTFLKLAF 191 QLLLFPTPGE 241 YPPTGGALSQ 291 PTGWSQSKTP 341 LSRIGSGSFG 391 HVNILLFMGY 441 TAQGMDYLHA 491 VEQPSGSILW 541 ASRDQIIYMV 591 ILSSIELLQH

Figure S2

Gene: ra

1 XXXXXXXXXX 51 FHTNRGAIKF 101 PNWHRDLVRV 151 KSNYNFEKPF 201 KVASETALPD

11 XXXXXXXXXX 61 NVWDTAGQEK 111 CENIPIVLCG 161 LWLARKLIGD 211 EEDDL

21 XXXXXXXXXX 71 FGGLRDGYYI 121 NKVDIKDRKV 171 PNLEFVAMPA

31 XXXXXXXXXA 81 QAQCAIIMFD 131 KAKSIVFHRK 181 LAPPEVSMDP


1

2

3

4

Positive selection

132

5

6

7

Purifying selection


41 TLGVEVHPLV 91 VTSRVTYKNV 141 KNLQYYDISA 191 SLAAQYEHDL

Figure S2

Gene: rb1

1 MPPKRRSAAP 51 VSLCQELRVT 101 AATDLDAMTF 151 LEKKYEVLLA 201 AKGNVLQMED 251 PTRTSRRGLG 301 AFLDSVGLAG 351 TDVSQLERTP 401 ENLVKYFSNC 451 LGVRLYYRVM 501 YDWSTFKSSS 551 MIKHLERCEH 601 LQHDHTAADL 651 LKSTSLSLFY 701 HELLKDRHLD 751 VLIREGQYDS 801 FSNSPLRVPG 851 RINQMVSSSD 901 QQKLAEMTST

11 SAQLSKAAED 61 DEVCNLAWKI 111 TITEVQKTVG 161 LFQRFERTCG 211 DLVISFQLLL 261 RGARAAPKPA 311 SQEIPESEDL 361 RKNPLEEEVL 411 TVNPSEEITE 461 ESMLRSEEER 511 SSSETDLSFP 561 LIMESIAWRS 611 YLSPVRSPWK 661 KKVYRLAYLR 711 QIMMSAMYAI 761 IIAFYNQVFM 811 SNNVYVSPLK 861 WSLKRGLESN 911 RTRMQEQKLK

21 KHTNRVGVPG 71 WETMVASVDI 121 LNVVEFFNLL 171 KIYIAVSDNA 221 CVLEYFIKRS 271 DTDLRVMEAL 321 SKQYEELYFK 371 PIPPQTPVRA 421 RVVNMRELFI 471 LSIQNFSKLL 521 WILDVFKLKA 571 DSPLFELLRQ 621 KSQSVASSAS 671 LNMLFSHLLK 721 CKVKNIDLRF 771 QKLKTNILQY 821 SARMSPSVMT 871 SAPKPLKRLR 921 DAAVDSLKEE

31 TPGRIPQLSL 81 VLLLGIKDTS 131 KKMDINMDTI 181 GNAGPDAKQI 231 PPTVLQEPFK 281 CKENECTVDE 331 SKDFDARLFL 381 AMNCIQQLKV 431 DRFARAVGQQ 481 SNADFHTSLL 531 FDFYKVIESF 581 SREQEGAVEQ 631 QGADAQTGPS 681 DHPELEHIIW 731 KTIVTAYKEL 781 ASPRPPTLSP 831 PRSRILVSIG 881 FDTDGQDEAD 931 KH


1

2

3

4

Positive selection

133

5

6

7

Purifying selection


41 ERHKDKEPPF 91 RKHWGACIFV 141 SVKVNTAVSR 191 MRSCWTLFLL 241 IAANGVHSTT 291 VKNVYFTSFV 341 DHDETLQPVK 391 ILNSASDWPS 441 CIEIGSQRFV 491 ACALEVVMAT 541 IKAEPSLTRE 591 AEPPGMLNQL 641 SQSQTSSHKH 691 TLFQHTLQHE 741 PNTHQETFKH 791 IPHIPCSPYK 841 ESFGTSEKFQ 891 GSKSAGESKF

Figure S2

Gene: r 1 MAAIRKKLVI 51 KQVELALWDT 101 PEVKHFCPNV 151 INAFGYLECS

11 VGDGACGKTC 61 AGQEDYDRLR 111 PIILVGNKKD 161 AKTKDGVREV

aa

21 LLIVFSKDQF 71 PLSYPDTDVI 121 LRNDEHTRRE 171 FEMATRAALQ

31 PEVYVPTVFE 81 LMCFSIDSPD 131 LAKMKQEPVK 181 AKKRGKKNAC


1

2

3

4

Positive selection

13

5

6

7

Purifying selection


41 NYVADIEVDG 91 SLENIPEKWT 141 PEEGRDMANR 191 LLL

Figure S2

Gene: r 1 MAAIRKKLVI 51 KQVPLNALKM 101 KHFCPNVPII 151 FGYMECSAKT

11 VGDGACGKTC 61 EIYDRLRPLS 111 LVGNKKDLRN 161 KDGVREVFEM

ab

21 LLIVFSKDQF 71 YPDTDVILMC 121 DEHTRRELAK 171 ATRAALQARR

31 PEVYVPTVFE 81 FSIDSPDSLE 131 MKQEPVKPEE 181 GKKTSKCLLL


1

2

3

4

Positive selection

13

5

6

7

Purifying selection


41 NYVADIEVDG 91 NIPEKWTPEV 141 GRDMANRIGA

Figure S2

Gene: r 1 MAAIRKKLVV 51 KQVELALWDT 101 PEVKHFCPNV 151 IGAYDYLECS

11 VGDGACGKTC 61 AGQEDYDRLR 111 PIILVANKKD 161 AKTKEGVREV

b

21 LLIVFSKDEF 71 PLSYPDTDVI 121 LRNDENVRNE 171 FETATRAALQ

31 PEVYVPTVFE 81 LMCFSVDSPD 131 LSRMKQEPVK 181 KRSRPSGGCL

41 NYVADIEVDS 91 SLENIPEKWV 141 TEDGRAMAVR 191 NCCKLL


1

2

3

4

Positive selection

13

5

6

7

Purifying selection

Likelihood ratio test between the null model (no positive selection) and the alternative model (enabling positive selection) shows a significance level of: 0.05


Figure S2

Gene: r 1 XQAQIKRRSG 51 TCEGSEPAVV 101 MPTPAFLSSL 151 FCSQCIRDCL

11 GSSRRPSKRR 61 DLTSNDSVVI 111 ESSNKARATP 161 RKASKCPTCR

21 RVTNAPPAME 71 VDEGLQGHRE 121 GTISCPICLD 171 KKLNYKQYHP

31 PETIEVLENN 81 ASGESYVLSS 131 TYGEIVGSGR 181 IYI


1

2

3

4

Positive selection

13

5

6

7

Purifying selection


41 LHSSEDVVDL 91 DEEEVEDSGM 141 LVVSTKCGHL

Figure S2

Gene: r 1 1 MSSEDLEAQE 51 KGEEHIKYPV 101 KRLDELWQEN 151 KEGAGKDNAE 201 DSKMFCCNIC 251 NCPEPECSSV 301 CETAVLVEPD 351 YLKASEEEKQ 401 VDGCNKMTCT 451 DDDEEFWSDE

11 DELLALASIY 61 SFLPTLILNF 111 VGSVVLFSWI 161 DTEKDSKEQP 211 FSEKMGSECT 261 ATPAQVKHLV 311 TTMGICPSCQ 361 FLEQRFGKRV 411 SCKQYFCWLC 461 ED

21 NEEEFHRAES 71 ELPSDYPSNS 121 QFLKEDLFSF 171 DPRAIQEVDP 221 CFKDCKHVYC 271 GEELFARYDR 321 YAFCTLCKMG 371 IQKAVEESFS 421 LGPLSRVNPY

31 AQGGEIRINL 81 PPVFTLSSRW 131 LSIESPLEVT 181 RSNLLLQLLD 231 KECMRDYFQI 281 LLLQSSLDLM 331 YHGLSPCRAT 381 SEWLEKNSKA 431 GHFNDTSSPC


1

2

3

4

Positive selection

13

5

6

7

Purifying selection


41 ELPQDFRIFA 91 LSRVQLGTLC 141 NSNKGKQERK 191 FDEMQQQKAF 241 QIRDGNVQCL 291 ADVMYCPRKM 341 AAELRGLRDE 391 CPRCSSNIQK 441 FNQLFQGVDI

Figure S2

Gene: rock1

1 MSAGESLEAR 51 SIDNFLNRYK 101 VYAMKLLSKF 151 MVMEYMPGGD 201 PDNMLLDKAG 251 GDGYYGRECD 301 DDSEISKDAK 351 TAAPVVPELS 401 SSNQLARGLS 451 EMEQKCRASN 501 YQRKAEQEAE 551 EEANDLLRVE 601 QLEKEVLQLQ 651 VETERKQAQE 701 LTDKYESIEE 751 LKQSVQKIEQ 801 DRMKGSEKQL 851 LVTAVSAQYF 901 SSCGSRRILC 951 EEVSATEKEE 1001 13

11 FEKIDAMLKD 61 DTISKIRDLR 111 EMIKRSDSAF 161 LVNLMSNYDV 211 HLKLADFGTC 261 WWSVGVFLYE 311 NLICAFLTDR 361 SDIDTSNFDD 411 TKTSEKRSSS 461 IKLDKIMKEL 511 KRRNVENEVS 561 SDTAARLRKS 611 AALESERRNW 661 RSNNLEKEKN 711 AKSATMQAVE 761 LMKQKERLEE 811 KQEMNTALEA 861 EKACLDDIKL 911 EWSRRMFRCR 961 LTNSVKAYYE 1011

21 PKSEVNTDCL 71 MKAEDYEVVK 121 FWEERDIMAF 171 PEKWARFYTA 221 MKMNQDGMVR 271 MLVGDTPFYA 321 EVRLGRNGVD 371 IEEDKGDEET 421 VKEDKSQLEN 471 DEETNLRKNM 521 TLKEQLEDMR 571 HTELTKSMSH 621 SQGSEEIQEL 671 NLEIDLNYKL 721 QKVSEESMAR 771 EVRSVRVQLE 821 KRSLEFQLAQ 871 GFNGFDSRAC 921 QLEETNKTLT 971 KILNTERTLK 1021

31 LDGLDALVYD 81 VIGRGAFGEV 131 ANSPWVVQLF 181 EVVLALDGIH 231 CDTAVGTPDY 281 DSLVGTYSKI 331 EIKRHPFFKN 381 FPIPKAFVGN 431 LQKRIYLLEE 481 DSTVSHLEKE 531 KISQNSQISN 581 LETVNRELQE 631 QGRITGLQED 681 KTLQQRLEHE 731 LKAENRVVEV 781 QESGRRVQAQ 831 LTNYSPDMSG 881 FSVAICFCTD 931 KDVENLSKEK 981 TQAVNKLAEI 1031


41 LDFPALRKNK 91 QLVRHKATRK 141 YAFQDDRYLY 191 SMGFIHRDVK 241 ISPEVLKSQG 291 MNHKNALTFP 341 DQWTWENIRE 391 QLPFVGFTYY 441 QLHSEMQLKD 491 KMMAQHRATE 541 DKITQLQKQL 591 KSRAADGARH 641 LKNLKLTLSK 691 LAEHAATKAR 741 EKQCSMLEFD 791 AELKTRAVEA 841 IFFPKTTHSS 891 EGGSCAGNIF 941 TELSEKMRVQ 991 MNRKDMKLDQ 1041

Figure S2

KKKGSTADLR 1051 ESTYRNELQM 1101 AESRLEGWLS 1151 VLDIDKLFHV 1201 QGEKTNCLPH 1251 KCHKDHLDRK 1301 PKTPPSSFTR

KKEKENRKLQ 1061 QLDSKESDIE 1111 IPNRANIKRY 1161 RPVTQGDVYR 1211 KGHEFIPTLY 1261 EDVIAPCKVN 1311 ASPRTMSTRS

LELNQEKEKF 1071 QLREKLNDLQ 1121 GWKKQYVVVS 1171 AETDEIPRIF 1221 HFPTNCEACA 1271 YDVTTARDML 1321 VANQSFRRNP

NHMAIKYQKE 1081 LRMDNSSVAS 1131 SKKILFYNDE 1181 QILYANEGEC 1231 KPLWHVFKPP 1281 LLALSQEEQK 1331 KSVTGKPR


1

2

3

4

Positive selection

1 0

5

6

7

Purifying selection


LSEMQAQLAE 1091 LQTDEADGNI 1141 QDKEQSNPSM 1191 RKDADTESVH 1241 PALECRRCHV 1291 KWIGHLGKKI

Figure S2

Gene: rock2

1 MSAGAERRME 51 NKNIETFLNR 101 QKVYAMKLLS 151 LYMVMEYMPG 201 VKPDNMLLDR 251 QGGDGYYGRE 301 FPDDVEISED 351 RETVAPVVPE 401 YFREDQLLSD 451 QSKDELDHKC 501 KNVEYQRKAE 551 QRQLDEVNSL 601 NAKLKLEKDF 651 SLSKAEMEKR 701 TKARLADKNK 751 CSMLDCDLKQ 801 KMQSQQVNAL 851 ELQDQLEAEQ 901 LAAQLEITLT 951 LAEKDATIGS 1001 1 1

11 NRLKKLEAMI 61 YEKVTGKIQD 111 KFEMIKRSDS 161 GDLVNLTSTY 211 HGHLKLADFG 261 CDWWSVGVFI 311 AKNLICAFLT 361 LSSDIDTSNF 411 SNPSAVENEH 461 RAACSRLEKV 511 NEADKKRCLE 561 LRTESDTAAR 611 ISLQSALESE 661 QLHERLTDFE 711 IYESIEEAKS 761 SHQKLEELRR 811 KMSEKQLKQE 861 YFSTLYKTQV 911 KADSEQLARS 961 LEEANRTLTS 1011

21 KDPRSLINLE 71 LQMKSEDYEV 121 AFFWEERDIM 171 DVPEKWAKFY 221 TCMKMDKTGM 271 FEMLVGDTPF 321 DREVRLGRSG 371 DEIEDDKGDV 421 RTSIKGEDSV 471 SKELDEEITS 521 NDVNSLRDQL 571 LRKTQTEMTK 621 KRDRNHGTEI 671 KEKSNIEIDM 721 EAMKEMEKKL 771 QKEKLTEEVK 821 INHLLEIKLS 871 RELKEECEEK 921 IAEEQYSDLE 971 DVANLANEKE 1021

31 SLLDSMNALV 81 VKVIGRGAFG 131 AFANSPWVVQ 181 TAEVVLALDA 231 VRCDTAVGTP 281 YADSLVGTYS 331 VEEIKRHPFF 381 ETFPVPKAFV 431 ASVQLQKKLH 481 RKHLESSLRQ 531 EDLKKRNQNS 581 QTQQLESNNR 631 ISDLQGRISG 681 TYKLKVLQQS 731 QEERSSKMKV 781 NLTLKIEQET 831 LEKQNSELRK 881 NKLCKEMQQK 931 KEKIMKELEI 981 ELNNRLKETQ 1031


41 LDLDFPALRK 91 EVQLVRHKAS 141 LCCAFQDDRY 191 IHSMGFIHRD 241 DYISPEVLKS 291 KIMDHKNSLN 341 KNDQWTFDTI 391 GNQLPFIGFT 441 QLEEQLNNEM 491 LEREKALLQH 541 QISNEKNIQL 591 ELQDKCCMLE 641 LEDELKHVKC 691 LEQEEAEHKA 741 ENILLEVEKQ 791 QKRSLTQNDL 841 ERQDADGQMK 891 LQELQDERDS 941 KEMMARHKQE 991 EQLQKAKEDE 1041

Figure S2

HSMALTKVQF 1051 RRKEKENRKL 1101 MALDSKDSDI 1151 WLSLPVRNNT 1201 FHVRPVTQTD 1251 SYICHKGHEF 1301 HMDKKEEVIA 1351 APDHFSRSSP

EKQLQSERTL 1061 QLELRSEREK 1111 EQLRSLLNSM 1161 KRFGWEKKYV 1211 VYRADAKEIP 1261 IPTLYHFPTN 1311 PCRVNYDVST 1361 RASMKVQPNQ

KTQAVNKLAE 1071 LNGTIIKYQK 1121 NVHGLDSASI 1171 VVSSKKILFY 1221 RIFQILYANE 1271 CEACTKPLWN 1321 AKNLLLLANS 1371 SIRRPSRQLP

IMNRKEVRGG 1081 EINEMQAQIA 1131 GSGPDFDSDE 1181 NNEQDKEQSN 1231 GESKKDQEFP 1281 MFKPPPALEC 1331 QEEQQKWVSR 1381 PNKPSTGPML


1

2

3

4

Positive selection

1 2

5

6

7

Purifying selection


ASRRGNDTDV 1091 DESQVRIELQ 1141 SYPDTTRLEG 1191 PYMVLDIDKL 1241 VEPLPIGEKS 1291 RRCHIKCHKD 1341 LVKKIPKKPP 1391 RIILH

Figure S2

Gene: rc 1 MGATKSKPKD 51 RRGNQSLTSN 101 YESRTASDLS 151 SIQAEEWYFG 201 DNTKGLNVKH 251 TEVCPVIKPQ 301 VAIKTLKPGT 351 GQGSLLDFLK 401 ILVGDNLVCK 451 KSDVWSFGIL 501 HELMLTCWRK

11 PGQRSRSLDG 61 AELVLFGGVD 111 FKKGERLQIV 161 KITRRDSERL 211 YKIRKLDSGG 261 TQGLARDAWE 311 MSTEAFLQEA 361 GDMGKILRLP 411 VADFGLARLI 461 LTELATKGRV 511 EPEERPTFEY

21 TIGIVGSYHP 71 SSIGITSPQR 121 NNTEGDWWLA 171 LLNLENRRGT 221 FYITSRTQFS 271 IPRESLRLDV 321 QVMKKLRHEK 371 QLVDMASQIA 421 EDNEYTARQG 471 PYPGMVNREV 521 LQSFLEDYFT

31 SHSPVQQTLT 81 VLIFLFSVTG 131 RSLTTGESGY 181 FLVRESETTK 231 NLQQLVSHYR 281 KLGQGCFGEV 331 LVQLYAVVSE 381 AGMAYVERMN 431 AKFPIKWTAP 481 LDQVERGYRM 531 STEPQYQPGE


1

2

3

4

Positive selection

1 3

5

6

7

Purifying selection


41 PNRSPAAEGS 91 GVTTFVALYD 141 IPSNYVAPSD 191 GAYCLSVLDY 241 KHADGLCHPL 291 WMGTWNGTTR 341 EPIYIVTEFM 391 YVHRDLRAAN 441 EAALYGRFTI 491 PCPAECPESL 541 NL

Figure S2

Gene: 1 XXXXXXXXXX 51 XXXXXXXXXX 101 XXXXXXXXXX 151 XXXXXXXXXX 201 DSMLGLLQSD 251 XXXXXXXXXX 301 XXXXXXXXXX 351 XXXXXXXXXX 401 CQACQEPIRG 451 CFIKLFG

11 XXXXXXXXXX 61 XXXXXXXXXX 111 XXXXXXXXXX 161 XXXXXXXXXX 211 LSRQGITTTA 261 XXXXXXXXXX 311 XXXXXXXXXX 361 XXXXXXXXSE 411 RCVTAMGAKF

b1 1

21 XXXXXXXXXX 71 XXXXXXXXXX 121 XXXXXXXXXX 171 XXXXXXXXXX 221 KGTCSACQKP 271 XXXXXXXXXX 321 XXXXXXXXXX 371 CYTPFVNGSF 421 HPQHLVCAFC

31 XXXXXXXXXX 81 XXXXXXXXXX 131 XXXXXXXXXX 181 PVLTSSRQAA 231 IVGQVXXXXX 281 XXXXXXXXXX 331 XXXXXXXXXX 381 FEHEGQPLCE 431 LKALSKGSFK


1

2

3

4

Positive selection

1

5

6

7

Purifying selection


41 XXXXXXXXXX 91 XXXXXXXXXX 141 XXXXXXXXXX 191 PPPQNPSGSL 241 XXXXXXXXXX 291 XXXXXXXXXX 341 XXXXXXXXXX 391 AHYHRSRGSV 441 EQDNKPYCQG

Figure S2

Gene: thrap3

1 MSKVPVSKSP 51 RSRSHSPPHN 101 YQRGGGYGNY 151 RSRRSGSSKR 201 RASGSWQGLI 251 AVKGGSPSPS 301 GFFSKDDVRA 351 ERDKGNGKAG 401 GPQFGSAEAG 451 NKWDELAYFP 501 KKAEASGYRG 551 DDSPPRSTPA 601 SKKDQEFRSI 651 NERFAMYQRR 701 SSKDEGKKMK 751 RERSTEKSSK 801 EEGFNKARLG 851 SNPGNPVRSK 901 QRGRGRFMFR 951 ATEQ

1

11 SRSRSGSGSR 61 RERNYPREYQ 111 RPNWQNYRQQ 161 NAAKELKESG 211 DYDTSPKRTS 261 RSSAAAQSKS 311 GEKPSSVSTA 361 SFDKGAAYSG 411 EDQEKRHKVR 461 SAKEKLRKEE 511 FSPDKAPKAS 561 YSGKRSAEVS 611 FQHIQSTQLR 661 AAEMMKPRKS 711 TDSMDLRLDI 761 HHKKTKKRKK 811 VRDYGGPMER 861 EEEWDPEYTP 911 KTSSSPKWTH

21 SPSRSFSRSR 71 NNREFRGYNR 121 PQQHHQHSPR 171 RPDSAAKEAQ 221 PAVRSAIIVS 271 LGNAPWQSSG 321 FKKFLEEHKN 371 LKPDYYSKNE 421 NQKEREMEDE 471 DAGEDDIDDV 521 RKKEKQGQSP 571 VRMDPFHEDY 621 RSPSELFAQH 671 PEIHRRIDVS 721 ERRKKYSSKE 771 TRERSRSSSE 821 GRGRGGFQFR 871 KSKKYYLHDD 921 DKFQGSGEEG

31 TRTRSRSRSR 81 GFRRPYYYRG 131 RGRSRSRSPK 181 RAGSRDEEAA 231 QGTAHPSPSL 281 PAPTSKSPPQ 331 KIQVAEWENG 381 EEKYGYDDEF 431 PKHKSKITIT 481 EEELYRSRKQ 531 SPPARKSSEN 581 ASSSGVLANE 631 IVTIVHHIKA 681 PSAFRKHSHL 731 REHKRDGMRD 781 SSSSSHSFKG 831 IRGRGWNRGN 881 REGEGEKKWV 931 ELPDDSDAEN


41 KHRYSSRSRS 91 RGRGYYPRGR 141 RRSGTPRSRS 191 GAAGGEGAPD 241 QSVAVKRPSP 291 QSPTAVFSGF 341 REKEQKMAEL 391 ELGSAAEFLK 441 ANRDMFDERF 491 ERAAAAAAAA 541 REREMFNVRR 591 RRFSRDLVHP 641 QHFESSGMTL 691 FEEMKSSRES 741 SGESRGSSLS 791 GDYPEGPEQK 841 YPGNNSNGNP 891 DNRGRGRGTF 941 KEEDKSGGTA

Figure S2 Legend: The selection scale:

1

2

3

4

Positive selection

1

5

6

7

Purifying selection


Figure S2

Gene: b 1 MKRAAAKHLI 51 ELYKINAKLC 101 DDFKDLNYLT 151 AKQHTKEELK 201 ATQGDNNVHK 251 VECDLTYHNV 301 PLPAQAKLVR 351 SVVAATKCLK 401 RRNKKGPRVD 451 FKVETENKFS 501 QQLNPYLRLK 551 EGGVSKEFFQ 601 IVLGLAIYNN 651 EYEGSVEEDM 701 YAEYILNKAV 751 FQALEETTEY 801 VGGLGKLKMI 851 TYAKGFGML

11 ERYYHQLTEG 61 DPHPSKKGTS 111 EEKVYEILEI 161 SLQGKDEDKD 211 LGPDEVSVDV 261 YSRDPNYLNL 311 LWSQYSAEQI 361 IVYYANVLGG 411 PLETELGVKT 461 FMTCPFILNA 511 VRRDHIIDDA 561 LVVEEIFNPD 611 CILDVHFPMV 661 MITFQISQTD 711 EKQFKAFRRG 761 DGGYNRDSRI 811 IAKNGPDTDR

a

21 CGNEACTNEF 71 SAYLENSAKG 121 CGEKEDYSPL 171 EDEKEKAACS 221 EAVRRVYNKL 271 FIIVMENSNL 321 RRMMETFQQL 371 DVDTDHNEEE 421 IDCRKPLIPF 471 VTKNLGLYYD 521 LVRLEMIAME 571 IGMFTYDETT 621 VYRKLMGKKG 671 LFGNPLMYDL 721 FHMVTNESPL 771 IKDFWDIVHA 821 LPTSHTCFNV

31 CASCPSFHRM 81 AHNNSCSDRK 131 IRVIGRVFSS 181 AAAAAMEEDS 231 LANEKIETAF 281 HSPEYLEIAL 331 ITYKVISNEF 381 DDEPIPESSE 431 EEFVNEPLND 481 NRIRMYSERR 531 NPADLKKQLY 581 KLFWFNPSSF 631 TFRDLADSHP 681 RENGDKIPVT 731 KYLFRPEEIE 781 FGEEQKRLFL 831 LLLPEYTTKE


1 1

2

3

4

5

6

7 T. Lorin, W. Salzburger & A. Böhne

41 DNNAAAVKAL 91 MNRKEAHAAR 141 AEGLVQSFRK 191 GASSSRIGDG 241 LNALVYLSPN 291 PLFCKAMSKL 341 NSRNLVNDDD 391 LTLQELLGEE 441 VLEMDKDYTF 491 ITVLYSLVQG 541 VEFEGEQGVD 591 ETEGQFTLIG 641 VLFQSLKELL 691 NENRKDFVTQ 741 LLICGSRNLD 791 QFTTGTDRAP 841 KLKERLLKAI

Figure S3 Resulting trees of branch-site model aBS-REL implemented in HyPhy allowing for different Ka/Ks ratios among sites and among branches for all retrieved genes of the AR signaling pathway. When available, the sequence of the spotted gar was used to root the tree, otherwise trees were rooted at the split of Otophysa from the other teleosts.

1


Figure S Resulting trees of branch-site model aBS-REL implemented in HyPhy (Version 2.2.4) allowing for different Ka/Ks ratios among sites and among branches. Visulaization over http://veg.github.io/hyphy-vision/absrel/ web interface

Ka/Ks selection scale for all pages of Figure S1 0 0.01 0.1

0.5 1

2

5

10

akt1

1


Figure S ar

arid1a

1 0


Figure S brca1

cav1

ccne1

1 1


Figure S cdc42

cdk7

1 2


Figure S cfl1l

ctnnb1

daxx

1 3


Figure S dnaja1

egfr

1


Figure S fhl2

fkbp4

1


Figure S flna

gnb2l1

grip1

1


Figure S kat5

limk2

mapk1

1


Figure S mapk3

med1

med4

1


Figure S med12

med13

1


Figure S med14

med16

med17

1 0


Figure S med24

med30

ncoa1

1 1


Figure S ncoa3

ncoa4

1 2


Figure S nkx3.1

nrip1

1 3


Figure S pias1

pias2

1


Figure S

pik3r1

pik3r2

1


Figure S pmepa1

ppap2a

ppargc1a

1


Figure S pten

1


Figure S ptk2a

ptk2b

1


Figure S ENSLOCG00000008397 ENSTNIG00000012875 ENSTRUG00000016765 ENSONIG00000019847 GI_584012219 GI_554845115 GI_499023276 GI_548338137 ENSGACG00000009531 ENSORLG00000003527 ENSXMAG00000011324 ENSPFOG00000015350 ENSXMAG00000011073 ENSPFOG00000015319 ENSXMAG00000011307 ENSPFOG00000015316 ENSXMAG00000011081 ENSTNIG00000017983 ENSTRUG00000016201 ENSORLG00000008763 ENSORLG00000008757 ENSPFOG00000004946 ENSXMAG00000001114 ENSGACG00000011601 ENSONIG00000017149 GI_583992724 GI_499014994 GI_554829712 GI_548382840 ENSONIG00000017151 GI_583992732 GI_554829718 GI_548382828 GI_499014998 ENSDARG00000099506 ENSDARG00000087954 ENSAMXG00000008935 ENSDARG00000074849 ENSDARG00000054649 ENSDARG00000013203 ENSDARG00000096666 ENSDARG00000096549

rac1

1


Figure S raf1

ran

rb1

1 0


Figure S rhoaa

rhoab

1 1


Figure S rhob

rnf4

1 2


Figure S rnf14

rock1

1 3


Figure S rock2

1


Figure S src

tgfb1i1

1


Figure S thrap3

ube3a

1


Table S1 Ray-finned fish genes of the non-genomic and genomic Androgen Receptor signaling pathway according to

NetPath, GO0030521, Bennett et al. 2010, Foradori et al. 2008

Gene

Species L.oculatus

AKT1

ENSLOCG00000012762

AR

ENSLOCG00000014680 ARA ARB ENSLOCG00000003798 ARID1AA ARID1AB ENSLOCG00000011391 BRCA1 ENSLOCG00000015597 CAV1 ENSLOCG00000005671 CCNE1

ENSLOCG00000001073 CDC42A CDC42B CDK7 CFL1L CTNNB1 DAXX

ARID1 BRCA1 CAV1 CCNE1

CDC4 CDK7 CFL1L CTNNB1 DAXX

Gene

Species D.rerio

A.mexicanus

G.aculeatus

ENSGACG00000006298 ENSTNIG00000019495

ENSTRUG00000013476 ENSPFOG00000010125 ENSXMAG00000006673 ENSORLG00000017024 gi_542229192

ENSDARG00000052004 ENSDARG00000098622

ENSAMXG00000009230 ENSAMXG00000012355 ENSAMXG00000013256 ENSAMXG00000011395 ENSAMXG00000020237 ENSAMXG00000013606 ENSAMXG00000015282 ENSAMXG00000011618 ENSAMXG00000002929

ENSGACG00000018525 ENSGACG00000020332 ENSGACG00000007244 ENSGACG00000007627 ENSGACG00000006381 ENSGACG00000009201 ENSGACG00000012549

ENSTNIG00000015783 ENSTNIG00000011826 ENSTNIG00000009659 ENSTNIG00000004670 ENSTNIG00000010246 ENSTNIG00000016057 ENSTNIG00000006196

ENSDARG00000044573 ENSDARG00000051916 ENSDARG00000012972 ENSDARG00000014571 ENSDARG00000000729

ENSAMXG00000019820 ENSAMXG00000003583 ENSAMXG00000008454 ENSAMXG00000007837 ENSAMXG00000000198 ENSAMXG00000014180

ENSGACG00000012448 ENSGACG00000010913 ENSGACG00000009848 ENSGACG00000004750 ENSGACG00000006037 ENSGACG00000001844

ENSTNIG00000012549 ENSTNIG00000007372 ENSTNIG00000015407

ENSTRUG00000005373 ENSTRUG00000012421 ENSTRUG00000013351 ENSTRUG00000012325 ENSTRUG00000009091 ENSTRUG00000017112 ENSTRUG00000000222 ENSTRUG00000000353 ENSTRUG00000001296 ENSTRUG00000001834 ENSTRUG00000001857 ENSTRUG00000017625 ENSTRUG00000000484 ENSTRUG00000013411 ENSTRUG00000000167 ENSTRUG00000010233

NM_001281801.1

ENSLOCG00000006117 ENSLOCG00000015680 ENSLOCG00000001383 ENSLOCG00000000498

ENSDARG00000067976 ENSDARG00000101710 ENSDARG00000101891

T.nigroviridis

ENSTNIG00000019094 ENSTNIG00000005315 ENSTNIG00000018185

DNAJA1

ENSLOCG00000011564 DNAJA1

ENSDARG00000030972 ENSAMXG00000010757 ENSGACG00000017879

EGFR

ENSLOCG00000011537 EGFRA EGFRB

gi_35903182

FHL2

ENSLOCG00000008763 FHL2A

ENSAMXG00000012474 ENSGACG00000017289 ENSTNIG00000014840 ENSAMXG00000015959 ENSGACG00000018079 ENSTNIG00000000023 ENSTNIG00000013552 ENSTNIG00000013553 ENSDARG00000003991 ENSAMXG00000005118 ENSGACG00000015048 ENSTNIG00000017175

FKBP4 FLNA GNB2I1

FHL2B ENSLOCG00000016880 FKBP4 ENSLOCG00000015505 FLNA ENSLOCG00000009758 GNB2I1

ENSDARG00000042018 ENSDARG00000008447 ENSDARG00000074201 ENSDARG00000041619

GRIP1 KAT5

ENSLOCG00000016167 GRIP1 NA KAT5

KDM3A LIMK2 MAPK1 MAPK3 MED1 MED4 MED12 MED13

ENSLOCG00000010817 ENSLOCG00000004821 ENSLOCG00000002024 NA ENSLOCG00000012767 ENSLOCG00000000694 ENSLOCG00000015382 ENSLOCG00000003727

MED14 MED16 MED17 MED24 MED30 NCOA1 NCOA3

ENSLOCG00000002286 ENSLOCG00000001808 ENSLOCG00000007406 ENSLOCG00000012864 ENSLOCG00000003235 ENSLOCG00000015891 ENSLOCG00000003989

NCOA4 NKX3.1 NR1I3 NRIP1

ENSLOCG00000012898 ENSLOCG00000015015 NA ENSLOCG00000000906

PIAS1

ENSLOCG00000013933 PIAS1A

PIAS2 PIK3R1 PIK3R2

PMEPA1 PPAP2A PPARGC1A PTEN PTK2A

PTK2B RAC1

KDM3A LIMK2 MAPK1 MAPK3 MED1 MED4 MED12 MED13A MED13B MED14 MED16 MED17 MED24 MED30 NCOA1 NCOA3A

NCOA3B NCOA4 NKX3.1 NR1I3 NRIP1A NRIP1B

ENSAMXG00000009663 ENSAMXG00000003846 ENSAMXG00000013411 ENSAMXG00000007457 ENSAMXG00000002584 ENSDARG00000015053 ENSAMXG00000011215 ENSDARG00000004587 ENSAMXG00000009091 ENSDARG00000045951 NA NA ENSDARG00000005104 gi_597735797 ENSDARG00000027552 ENSAMXG00000001222 ENSDARG00000070573 ENSAMXG00000017822 ENSDARG00000075340 ENSAMXG00000015432 ENSDARG00000041503 ENSAMXG00000012890 ENSDARG00000056800 ENSAMXG00000011603 ENSDARG00000053884 ENSAMXG00000000953 ENSDARG00000003910 ENSAMXG00000002817 ENSDARG00000009953 ENSAMXG00000002581 ENSDARG00000040779 ENSAMXG00000018838 ENSDARG00000006345 ENSAMXG00000016638 ENSDARG00000032459 ENSAMXG00000012180 ENSDARG00000029459 ENSAMXG00000021203 ENSDARG00000018257 ENSAMXG00000010390 ENSAMXG00000008788 ENSAMXG00000008791 ENSAMXG00000008794 ENSDARG00000077404 ENSAMXG00000006902 ENSDARG00000021439 ENSAMXG00000015735 ENSDARG00000078280 ENSAMXG00000024837 NA NA ENSDARG00000068965 ENSAMXG00000025365 ENSDARG00000068894 ENSAMXG00000025737

ENSGACG00000003005 ENSGACG00000012979 ENSGACG00000013098 ENSGACG00000018103

ENSTNIG00000000462 NA ENSTNIG00000004951 ENSTNIG00000010510

T.rubripes

P.formosa

X.maculatus

O.niloticus

N.brichardi M.zebra

A.burtoni

Source of gene

gi_498935125 gi_548423349

gi_554812288

NetPath, Bennett et al 2010, Foradori et al 2008 non-genomic, genomic

gi_499025148 gi_499011353 gi_499018427 gi_499027400 gi_499033693 gi_499007024 gi_499030053

gi_545793521 gi_548397957 gi_548435329 gi_548538463 gi_548541303 gi_548521455 gi_548348207

gi_555943746 gi_555943801 gi_554870576 gi_554835101 gi_554835497 gi_554856484 gi_554826914

NetPath NetPath GO:0030521 GO:0030521 NetPath, GO:0030521 NetPath NetPath, GO:0030521

receptor, genomic, non-genomic receptor, genomic, non-genomic genomic genomic genomic, positive regulator non-genomic genomic, positive regulator

gi_573898313 gi_494461779 gi_545793478 gi_584010624 gi_499018345 gi_548348712 gi_583977761 gi_498955997 gi_548339440 gi_584024814 no blast hit on ntgi_548490653 gi_583999804 gi_499034959 gi_548426098 gi_573898112 gi_499044186 gi_548490874

gi_545786543 gi_554846439 gi_554874678 gi_554852342 gi_554880769 gi_554886315

NetPath NetPath GO:0030521 NetPath NetPath, GO:0030521 NetPath, GO:0030521

non-genomic non-genomic genomic non-genomic genomic, positive regulator genomic, negative regulator

gi_583981523

ENSPFOG00000006490 ENSPFOG00000019378 ENSPFOG00000009717 ENSPFOG00000002208 ENSPFOG00000004731 ENSPFOG00000014440 ENSPFOG00000011801

ENSXMAG00000002896 ENSXMAG00000012307 ENSXMAG00000010716 ENSXMAG00000012041 ENSXMAG00000009949 ENSXMAG00000014453 ENSXMAG00000001005

ENSORLG00000008220 ENSONIG00000017538 gi_583972812 ENSORLG00000009520 ENSONIG00000012854 gi_584009291 ENSORLG00000004410 ENSONIG00000006764 gi_584001874 ENSONIG00000007618 gi_584000591 ENSORLG00000004585 ENSONIG00000016326 gi_583992196 ENSORLG00000019746 ENSONIG00000003896 gi_583973968 ENSORLG00000015511 ENSONIG00000003504 gi_584015275

ENSPFOG00000005335 ENSPFOG00000004608 ENSPFOG00000017422 ENSPFOG00000017145 ENSTRUG00000003520 ENSPFOG00000018568 ENSTRUG00000003811 ENSPFOG00000001776

ENSXMAG00000016228 ENSXMAG00000008839 ENSXMAG00000007316 ENSXMAG00000006139 ENSXMAG00000008710 ENSXMAG00000007090

ENSORLG00000013756 ENSORLG00000012048 ENSORLG00000008836 ENSORLG00000011865 ENSORLG00000005845 ENSORLG00000006837

ENSONIG00000016914 ENSONIG00000020235 ENSONIG00000013709 ENSONIG00000010009 ENSONIG00000007226 ENSONIG00000008401

P.nyererei

gi_498979425 gi_548348922

gi_554873916

GO:0030521

genomic

gi_498945991 gi_548422483 gi_499050178 gi_548511931

gi_554803235 gi_545785452

NetPath NetPath

non-genomic non-genomic

ENSTRUG00000008468 ENSPFOG00000003291 ENSPFOG00000022124 ENSPFOG00000015302 ENSPFOG00000018881 ENSPFOG00000001616 ENSPFOG00000008165

ENSXMAG00000002166 ENSORLG00000001848 ENSONIG00000012307 gi_583995557

gi_499025292 gi_548401457

gi_554818515

NetPath, GO:0030521

genomic, positive regulator

ENSXMAG00000011596 ENSXMAG00000003963 ENSXMAG00000004665 ENSXMAG00000008940

gi_498986713 gi_498994696 gi_498964459 gi_498935526

gi_548379261 gi_548356125 gi_548536083 gi_548334125

gi_554870366 gi_545786431 gi_554815264 gi_554821010

NetPath, GO:0030521 GO:0030521 NetPath NetPath

genomic, positive regulator genomic, negative regulator non-genomic genomic

ENSTRUG00000013559 ENSTRUG00000015044 ENSTRUG00000003170 ENSTRUG00000000550

ENSORLG00000012482 ENSORLG00000008977 ENSORLG00000001982 ENSORLG00000005276

ENSONIG00000014220 ENSONIG00000015051 ENSONIG00000017914 ENSONIG00000012984

gi_583986192 gi_583988484 gi_584019220 gi_583972285

ENSGACG00000000177 ENSTNIG00000002863 ENSGACG00000020408 ENSTNIG00000011743

ENSTRUG00000005225 ENSPFOG00000012379 ENSXMAG00000006468 ENSORLG00000017453 gi_542204218 gi_583971256 ENSTRUG00000016643 ENSPFOG00000010293 ENSXMAG00000005173 ENSORLG00000007458 ENSONIG00000005359 gi_584015024

gi_499031622 gi_548419148 gi_499026510 gi_548385825

gi_554820840 gi_554823092

GO:0030521 NetPath, GO:0030521

genomic genomic, positive regulator

NA ENSGACG00000008716 ENSGACG00000014421 ENSGACG00000013102 ENSGACG00000006033 ENSGACG00000008017 ENSGACG00000017493 ENSGACG00000020213 ENSGACG00000010389 ENSGACG00000002015 ENSGACG00000013385 ENSGACG00000013203 ENSGACG00000008529 ENSGACG00000003014 ENSGACG00000006727 ENSGACG00000015221

NA ENSTNIG00000015862 ENSTNIG00000015351 ENSTNIG00000011583 ENSTNIG00000004334 ENSTNIG00000003778 ENSTNIG00000015746 ENSTNIG00000009033 ENSTNIG00000003289 ENSTNIG00000014969 ENSTNIG00000004736 ENSTNIG00000006440 ENSTNIG00000012846 ENSTNIG00000000448 ENSTNIG00000019142 ENSTNIG00000012601

NA ENSTRUG00000013732 ENSTRUG00000015300 ENSTRUG00000005697 ENSTRUG00000012065 ENSTRUG00000014013 ENSTRUG00000012646 ENSTRUG00000008851 ENSTRUG00000007405 ENSTRUG00000013609 ENSTRUG00000007850 ENSTRUG00000004276 ENSTRUG00000016382 ENSTRUG00000003806 ENSTRUG00000006619 ENSTRUG00000004450

NA ENSPFOG00000009526 ENSPFOG00000006212 ENSPFOG00000008154 ENSPFOG00000001519 ENSPFOG00000010829 ENSPFOG00000000954 ENSPFOG00000024209 ENSPFOG00000009647 ENSPFOG00000013987 ENSPFOG00000008857 ENSPFOG00000017880 ENSPFOG00000016585 ENSPFOG00000000737 ENSPFOG00000004231 ENSPFOG00000011587

NA ENSXMAG00000018076 ENSXMAG00000006444 ENSXMAG00000011987 ENSXMAG00000002969 ENSXMAG00000008718 ENSXMAG00000000274 ENSXMAG00000000108 ENSXMAG00000018016 ENSXMAG00000018007 ENSXMAG00000010740 ENSXMAG00000007752 ENSXMAG00000011374 ENSXMAG00000014029 ENSXMAG00000017782 ENSXMAG00000017470

NA NA ENSORLG00000006835 ENSONIG00000013399 ENSONIG00000014115 scaffold5487_contig129853 ENSORLG00000011993 ENSONIG00000019408 ENSORLG00000008300 gi_542192331 ENSORLG00000014076 ENSONIG00000016177 ENSORLG00000000784 ENSONIG00000002455 ENSORLG00000012337 ENSONIG00000017544 ENSORLG00000005489 ENSONIG00000011173 ENSORLG00000010808 ENSONIG00000006848 ENSORLG00000000109 ENSONIG00000004564 ENSORLG00000000709 ENSONIG00000001372 ENSORLG00000008227 ENSONIG00000019926 ENSORLG00000001732 ENSONIG00000013534 scaffold1294_contig113045ENSONIG00000015724 ENSORLG00000012143 ENSONIG00000017075

NA gi_498956642 gi_499004332 gi_499019863 gi_499021221 gi_499031293 gi_498964171 gi_499021858 gi_499014114 gi_499034639 gi_499010815 gi_499047177 gi_499023404 gi_498976995 gi_498984261 gi_498965809



GO:0030521 NetPath Bennett et al 2010 Bennett et al 2010 GO:0030521 GO:0030521 GO:0030521 GO:0030521 GO:0030521 GO:0030521 GO:0030521 GO:0030521 GO:0030521 GO:0030521 NetPath, GO:0030521 NetPath, GO:0030521

genomic non-genomic non-genomic, genomic non-genomic, genomic genomic genomic genomic genomic genomic genomic genomic genomic genomic genomic genomic, positive regulator genomic, positive regulator

ENSGACG00000010036 ENSGACG00000012317 ENSGACG00000010776 NA

ENSTNIG00000007303 ENSTNIG00000013384 SCAF14652 NA

ENSTRUG00000009516 ENSTRUG00000003924 NA NA

ENSPFOG00000006902 ENSPFOG00000005630 ENSPFOG00000009654 NA

ENSXMAG00000001970 ENSXMAG00000002456 ENSXMAG00000020262 NA

ENSORLG00000013704 ENSORLG00000003269 ENSORLG00000010925 NA

gi_499042642 gi_548447463 gi_499046546 gi_548457815 gi_498955057 gi_548354440

gi_554808986 gi_554883384 gi_554824085

NetPath, GO:0030521 NetPath, GO:0030521 GO:0030521 GO:0030521 GO:0030521 GO:0030521

genomic, positive regulator genomic, positive regulator genomic genomic genomic genomic

ENSGACG00000020154


ENSONIG00000020313 gi_583978807 ENSONIG00000007129 gi_584024662 ENSONIG00000011762 gi_583977526 NA

ENSTRUG00000004236 ENSPFOG00000017715 ENSXMAG00000014033 ENSORLG00000000586 ENSONIG00000015866 gi_584025409 ENSTRUG00000000031 ENSTRUG00000016843 ENSPFOG00000006900 ENSXMAG00000017552 ENSORLG00000002077 ENSONIG00000013251 gi_583997712

gi_499021768 gi_548408144

gi_554851579

gi_499013515 gi_548448896

gi_554840096

PIAS1B ENSLOCG00000006647 PIAS2 ENSLOCG00000010510 PIK3R1A PIK3R1B ENSLOCG00000001519 PIK3R2A

ENSDARG00000036094 ENSAMXG00000006151 ENSGACG00000016894 ENSTNIG00000003928 ENSTNIG00000009549 ENSDARG00000062445 ENSAMXG00000002784 ENSGACG00000005176 ENSTNIG00000008434 ENSDARG00000092979 ENSAMXG00000002435 ENSGACG00000005099 ENSTNIG00000003200 ENSDARG00000038524 ENSAMXG00000011959 ENSGACG00000015820 ENSTNIG00000013464 ENSGACG00000001062 ENSTNIG00000018878 ENSDARG00000018060 XM_007236673.1 ENSGACG00000008201 ENSTNIG00000010197

ENSTRUG00000015008 ENSTRUG00000013569 ENSTRUG00000007584 ENSTRUG00000010930 ENSTRUG00000007054

PIK3R2B PMEPA1 PPAP2A PPARGC1A PTENA PTENB ENSLOCG00000007702 PTK2AA

NA ENSDARG00000039325 ENSDARG00000053381 ENSDARG00000067829 ENSDARG00000071018 ENSDARG00000056623 ENSDARG00000040197

NA ENSAMXG00000013100 ENSAMXG00000018732 ENSAMXG00000002461 ENSAMXG00000010994 ENSAMXG00000007753 ENSAMXG00000018637

PTK2AB ENSLOCG00000017241 PTK2BB PTK2BA ENSLOCG00000008397 RAC1AA

ENSDARG00000004672 ENSDARG00000039577 ENSDARG00000022841 ENSDARG00000074849 ENSDARG00000099506 ENSDARG00000087954 ENSDARG00000013203 ENSDARG00000096666 ENSDARG00000096549 ENSDARG00000054649

ENSAMXG00000004491 ENSAMXG00000019303 ENSAMXG00000000798 ENSAMXG00000008935

NA NA ENSLOCG00000012350 ENSLOCG00000006145

RAC1B

Pathway association

ENSPFOG00000004920 ENSXMAG00000005855 ENSORLG00000006260 ENSONIG00000014539 gi_583983886 ENSPFOG00000005099 ENSTRUG00000011834 ENSPFOG00000008848 ENSXMAG00000016482 ENSORLG00000017692 ENSONIG00000009358 gi_583994068 ENSTRUG00000017446 ENSPFOG00000005185 ENSXMAG00000008804 ENSORLG00000003577 ENSONIG00000017327 gi_584029670

ENSGACG00000015520 ENSGACG00000003728 NA ENSGACG00000019546 ENSGACG00000009998 ENSGACG00000009236 ENSGACG00000004011 ENSGACG00000004003 ENSGACG00000007004 ENSGACG00000010609 ENSGACG00000014838 ENSGACG00000011601

ENSTNIG00000011070 NA NA ENSTNIG00000002174 ENSTNIG00000005984 ENSTNIG00000013318 ENSTNIG00000009167 ENSTNIG00000009166 ENSTNIG00000009636 ENSTNIG00000016347 ENSTNIG00000014508 ENSTNIG00000017983

NetPath, GO:0030521

genomic, negative regulator

ENSXMAG00000003583 scaffold_JH558015.1 ENSXMAG00000018595 ENSXMAG00000015104 ENSXMAG00000002484

ENSORLG00000006728 ENSORLG00000017353 ENSORLG00000002670 ENSORLG00000017457 LOC101163728

ENSONIG00000015473 ENSONIG00000013927 ENSONIG00000011065 ENSONIG00000001749 ENSONIG00000012700

gi_583988189 gi_584015665 gi_584003878 gi_573878953 gi_583993919

gi_498993905 gi_499015732 gi_498981102 gi_499049716 gi_499028291

gi_548355942 gi_548377776 gi_548334788 gi_548541918 gi_548356312

gi_554863406 gi_554864979 gi_554838849 gi_554876860 gi_554849340

NetPath, GO:0030521 NetPath, GO:0030521 NetPath, Bennett et al 2010, Foradori et al 2008 NetPath, Bennett et al 2010, Foradori et al 2008 NetPath, Bennett et al 2010, Foradori et al 2008

genomic, negative regulator genomic, negative regulator non-genomic non-genomic non-genomic

ENSTRUG00000010476 NA NA ENSTRUG00000007210 NA ENSTRUG00000009851 ENSTRUG00000007362

ENSPFOG00000009110 ENSPFOG00000000261 ENSPFOG00000001009 ENSPFOG00000015835 ENSPFOG00000000170 ENSPFOG00000023056 ENSPFOG00000024225 ENSPFOG00000003942 ENSPFOG00000001516 ENSPFOG00000003517 ENSPFOG00000001263 ENSPFOG00000004955 ENSPFOG00000015747 ENSPFOG00000003397

ENSXMAG00000013889 ENSXMAG00000010456 ENSXMAG00000004780 ENSXMAG00000007748 ENSXMAG00000014454 ENSXMAG00000012957 ENSXMAG00000015476

NA ENSONIG00000010477 ENSORLG00000012800 ENSONIG00000004438 ENSORLG00000005464 ENSONIG00000007599 ENSORLG00000004788 ENSONIG00000007635 ENSORLG00000020711 ENSONIG00000019123 ENSORLG00000006231 ENSONIG00000000386 ENSONIG00000002815 scaffold5001_contig128876

gi_583983019 gi_573906092 gi_583987884 gi_584018961 gi_583996646 gi_583976942 gi_583985834

gi_498942969 gi_494461325 gi_498980257 gi_498999424 gi_499029140 gi_498987823 gi_498978332

gi_548336831 gi_545793510 gi_548335165 gi_548425231 gi_548428164 gi_548350440 gi_548352657

gi_554819907 gi_545786152 gi_554813089 gi_554850044 gi_554877417 gi_554806495 gi_554813630

NetPath, Bennett et al 2010, Foradori et al 2008 GO:0030521 GO:0030521 GO:0030521 NetPath NetPath NetPath

non-genomic genomic genomic genomic non-genomic non-genomic non-genomic

ENSTRUG00000011167 ENSTRUG00000008406 ENSTRUG00000017337 ENSTRUG00000016201

ENSPFOG00000010090 ENSPFOG00000008438 ENSPFOG00000009145 ENSPFOG00000004946

ENSXMAG00000010911 ENSXMAG00000004048 ENSXMAG00000004406 ENSXMAG00000001114

ENSORLG00000004751 ENSORLG00000008993 ENSORLG00000005884 ENSORLG00000008757 ENSORLG00000008763

gi_573896657 gi_584004629 gi_584025201 gi_583992724

gi_499029030 gi_498939798 gi_499049776 gi_499014994

gi_548435043 gi_548381009 gi_545793246 gi_548382840

gi_554849438 gi_554807097 gi_554877844 gi_554829712

NetPath NetPath NetPath NetPath

non-genomic non-genomic non-genomic non-genomic

RAC1AB

1

O.latipes

ENSGACG00000009531 ENSTNIG00000012875

ENSTRUG00000016765 ENSPFOG00000015316 ENSXMAG00000011073 ENSPFOG00000015319 ENSXMAG00000011081 ENSPFOG00000015350 ENSXMAG00000011307 ENSXMAG00000011324

ENSONIG00000006838 ENSONIG00000015297 ENSONIG00000015175 ENSONIG00000017149

ENSORLG00000008757 ENSONIG00000017151 gi_583992732 ENSORLG00000008763 ENSORLG00000003527 ENSONIG00000019847 gi_584012219


gi_499014998 gi_548382828

gi_554829718

NetPath

non-genomic

gi_499023276 gi_548338137

gi_554845115

NetPath

non-genomic

RAF1

ENSLOCG00000013974 RAF1

RAN RB1 RHOAA

ENSLOCG00000008279 RAN ENSLOCG00000008882 RB1 ENSLOCG00000014301 RHOAAA RHOAAB ENSLOCG00000014438 RHOABA RHOABB ENSLOCG00000017876 RHOB ENSLOCG00000006957 RNF4 ENSLOCG00000010578 RNF14A RNF14B

RHOAB RHOB RNF4 RNF14

ROCK1 ROCK2

ENSLOCG00000001989 ROCK1 ENSLOCG00000016666 ROCK2A

TGFB1I1 THRAP3

ROCK2B NA SCGB2A1 ENSLOCG00000002309 SRCA SRCB Scaffold_JH591692.1 TGFB1I1 ENSLOCG00000002939 THRAP3A

UBE3A

THRAP3B ENSLOCG00000008388 UBE3A

SCGB2A1 SRC

1

ENSDARG00000059406 ENSDARG00000096415 ENSDARG00000057026 ENSDARG00000006782 ENSDARG00000026845 ENSDARG00000015429 ENSDARG00000094673

ENSAMXG00000005440 ENSGACG00000000060 ENSTNIG00000012621 ENSAMXG00000001055 ENSAMXG00000015390 ENSGACG00000017755 ENSTNIG00000013137 ENSAMXG00000005363 ENSGACG00000020379 ENSTNIG00000011786 ENSAMXG00000014632 ENSGACG00000009938 ENSTNIG00000015015 ENSAMXG00000005847 ENSGACG00000005670 ENSTNIG00000006051 ENSAMXG00000008373 ENSGACG00000001206 ENSTNIG00000014672 ENSAMXG00000026330 ENSGACG00000009667 ENSTNIG00000002278 ENSDARG00000090993 ENSAMXG00000007606 ENSGACG00000016217 SCAF7445 ENSDARG00000002794 ENSAMXG00000020091 ENSGACG00000020731 ENSTNIG00000018203 ENSDARG00000043905 ENSGACG00000006180 ENSTNIG00000006782 ENSDARG00000078683 ENSDARG00000090710 ENSDARG00000091727 ENSDARG00000058993 ENSAMXG00000014672 ENSGACG00000017327 ENSTNIG00000008471 ENSDARG00000017500 ENSAMXG00000021207 ENSGACG00000012788 ENSTNIG00000008912 ENSDARG00000004877 ENSAMXG00000003869 ENSGACG00000009555 NA NA NA ENSAMXG00000014517 ENSGACG00000005548 ENSDARG00000008107 ENSAMXG00000001275 ENSGACG00000011349 ENSAMXG00000020290 ENSGACG00000007235 ENSDARG00000040095 ENSAMXG00000001863 ENSGACG00000013745 ENSDARG00000044459 ENSDARG00000003513 ENSAMXG00000020877 ENSGACG00000002319 ENSDARG00000055737 ENSAMXG00000012931 ENSGACG00000015321

ENSTRUG00000006611

ENSPFOG00000015974 ENSXMAG00000017691 ENSORLG00000011471 ENSONIG00000017170 gi_584003028

ENSTRUG00000013749 ENSPFOG00000009552 ENSXMAG00000009922 ENSTRUG00000015842 ENSPFOG00000003889 ENSXMAG00000015729 ENSPFOG00000017531 ENSXMAG00000004466 ENSTRUG00000010405 ENSTRUG00000010942 ENSPFOG00000000160 ENSXMAG00000019368 ENSTRUG00000011944 ENSPFOG00000019065 ENSXMAG00000016892 ENSTRUG00000018178 ENSPFOG00000020611 ENSXMAG00000019632 ENSTRUG00000017344 ENSPFOG00000017123 ENSXMAG00000015165 ENSTRUG00000008815 ENSPFOG00000006823 ENSXMAG00000001585 ENSTRUG00000004900 ENSPFOG00000019210 ENSXMAG00000002519

gi_498965606 gi_548483383

gi_554857802

Foradori et al 2008

non-genomic

ENSORLG00000003452 ENSONIG00000005139 gi_583972026 gi_498962091 gi_548341336 ENSORLG00000008317 ENSONIG00000004276 gi_584014918 gi_499026357 gi_548387323 ENSONIG00000017974 gi_584019304 gi_498964222 gi_548443896 ENSONIG00000012367 gi_583980905 gi_499016231 gi_548370620 ENSORLG00000002742 ENSONIG00000001670 gi_583980256 gi_498997689 gi_548357349 ENSORLG00000018734 ENSONIG00000018884 gi_583976140 gi_498957597 gi_548414713 ENSORLG00000012619 ENSONIG00000020448 gi_583994917 gi_499036281 gi_548358324 ENSORLG00000020573 gi_542256685 gi_583973152 gi_499025880 gi_548333174 ENSORLG00000001462 ENSONIG00000008460 gi_583979411 gi_498982921 gi_548351054 ENSORLG00000011566

gi_554805068 gi_554822936 gi_554866988 gi_554807569 gi_554857836 gi_554862978 gi_554821869 gi_554877732 gi_545785817

NetPath, GO:0030521 NetPath, GO:0030521 NetPath NetPath NetPath NetPath NetPath NetPath, GO:0030521 GO:0030521 GO:0030521

genomic, positive regulator genomic, positive regulator non-genomic non-genomic non-genomic non-genomic non-genomic genomic, positive regulator genomic genomic

gi_554803283 gi_545786390

NetPath NetPath

non-genomic non-genomic

gi_548358264 NA gi_548355415 gi_548412532 gi_548490449 gi_548389984

gi_554821891 NA gi_554866558 gi_554816133 gi_554875222 gi_554830071

NetPath GO:0030521 NetPath, Bennett et al 2010, Foradori et al 2008 NetPath, Bennett et al 2010, Foradori et al 2008 NetPath, GO:0030521 GO:0030521

non-genomic genomic non-genomic non-genomic genomic, positive regulator genomic

gi_498976772 gi_548406882 gi_499026835 gi_548467978

gi_554857382 gi_554857247

GO:0030521 NetPath, GO:0030521

genomic genomic, positive regulator

ENSTNIG00000012308 NA ENSTNIG00000018270 ENSTNIG00000019527 ENSTNIG00000018936 ENSTNIG00000012194

ENSTRUG00000013281 ENSPFOG00000011127 ENSTRUG00000010769 ENSPFOG00000012091 ENSPFOG00000012199 ENSTRUG00000018218 ENSPFOG00000019296 NA NA ENSTRUG00000018366 ENSPFOG00000013135 ENSTRUG00000005980 ENSPFOG00000000684 ENSTRUG00000005520 ENSPFOG00000007368 ENSTRUG00000010702 ENSPFOG00000013297

ENSXMAG00000002398 ENSORLG00000017642 gi_542206027 ENSXMAG00000009185 ENSORLG00000018255 gi_542208870

gi_583994033 gi_584008970

ENSXMAG00000013653 NA ENSXMAG00000010238 ENSXMAG00000001476 ENSXMAG00000018458 ENSXMAG00000014797

gi_583995367 gi_499036295 NA NA gi_583974949 gi_498971516 gi_583997963 gi_499019153 gi_584022201 gi_499048970 gi_583993177 gi_498985480

ENSTNIG00000004582 ENSTNIG00000014475

ENSTRUG00000010336 ENSPFOG00000000525 ENSXMAG00000017962 ENSORLG00000009543 ENSONIG00000013673 gi_583998686 ENSTRUG00000006347 ENSPFOG00000018875 ENSXMAG00000009731 ENSORLG00000020667 ENSONIG00000003746 gi_584015939

ENSORLG00000012731 NA ENSORLG00000006714 ENSORLG00000016183 ENSORLG00000005775 ENSORLG00000014550

gi_542255251 NA ENSONIG00000006882 ENSONIG00000016547 ENSONIG00000011521 gi_542234433


gi_498945850 gi_548422536 gi_499017063 gi_548401842

Table S2 Results of jmodeltest on each coding sequence alignment indicating the best fitting nucelotide substitution model per gene Tree akt1 ar arid1a brca1 cav1 ccne1 cdc42 cdk7 cfl1l ctnnb1 daxx dnaja1 egfr fhl2 fkbp4 flna gnb2l1 grip1 kat5 limk2 mapk1 mapk3 med1 med4 med12 med13 med14 med16 med17 med24 med30 ncoa1 ncoa3 ncoa4 nkx3-1 nrip1 pias1 pias2 pik3r1 pik3r2 pmepa1 ppap2a ppargc1a pten ptk2a ptk2b rac1 raf1 ran rb1 rhoaa rhoab rhob rnf14 rnf4 rock1 rock2 src tgfb1i1 thrap3 ube3a

1

Best model according to AICc GTR+G GTR+G+I GTR+G+I GTR+G+I HKY+I GTR+G+I SYM+G+I GTR+G+I GTR+G GTR+G+I GTR+G+I GTR+G+I GTR+G+I GTR+G GTR+G+I GTR+G+I GTR+G+I GTR+G GTR+G+I GTR+G+I GTR+G+I GTR+G GTR+G+I GTR+G GTR+G+I GTR+G+I GTR+G+I GTR+G+I GTR+G+I GTR+G+I HKY+G HKY+G GTR+G+I GTR+G+I HKY+G+I GTR+G+I HKY+G+I GTR+G+I GTR+G+I GTR+G+I HKY+G+I GTR+G GTR+G GTR+G+I GTR+G GTR+G+I SYM+G GTR+G+I SYM+G+I HKY+G GTR+G+I GTR+G+I HKY+G GTR+G+I GTR+G+I GTR+G+I GTR+G+I GTR+G+I GTR+G GTR+G+I GTR+G+I


Table S3 p-values of two-sided Welch's t-test of Ka/Ks comparisons Lake cichlids vs. Nile tilapia for TSGD gene copy A vs. gene copy B as shown in Figure 3 Gene ar arid1a cdc42 egfr fhl2 med13 ncoa3 pias1 pik3r1 pik3r2 pten ptk2a ptk2b rac1a rhoaa rhoab rock2 src thrap3

1 0

p-value 1.26E-06 0.3198596 NA 0.1058882 0.0004413 0.0017968 0.0335987 0.0003377 0.0240627 0.0063452 0.0122406 0.3775205 7.81E-05 7.16E-06 0.0052176 NA 0.0003164 0.0040781 0.0004625


Table S4 p-values of two-sided Welch's t-test for comparisons of testis as shown in Figure 4 Tissue Brain Brain Brain Brain Ovary Ovary Ovary Ovary Testis Testis Testis Testis

1 1

Species A. burtoni E. cyanostictus J. ornatus O. ventralis A. burtoni E. cyanostictus J. ornatus O. ventralis A. burtoni E. cyanostictus J. ornatus O. ventralis

values of TSGD duplicate genes in four cichlid species in brain, ovary and

Gene ar

cdc42

egfr

med13 pik3r1 pik3r2

pten

ptk2a

ptk2b

rac1a

rhoaa

rhoab

rock2

src

thrap3 arid1a fhl2a

ncoa3

pias1

0.00346 0.00045 0.01436 0.00024 0.40845 0.03572 0.20389 0.01364 0.01080 0.75190 0.78731 0.02149

0.05275 0.00008 0.00000 0.03156 0.30001 0.00000 0.00011 0.01686 0.00154 0.00007 0.00002 0.00885

0.00049 0.00006 0.00075 0.00004 0.29335 0.01759 0.03002 0.92110 0.08909 0.00501 0.00000 0.06161

0.00000 0.00001 0.00000 0.00003 0.08093 0.14124 0.11506 0.44459 0.00005 0.29676 0.00006 0.06250

0.01560 0.00000 0.00000 0.00000 0.02884 0.06825 0.00926 0.19111 0.00328 0.02637 0.76850 0.03967

0.13330 0.10212 0.66626 0.01268 0.02092 0.24108 0.02540 0.00001 0.00055 0.00001 0.00885 0.00582

0.01368 0.01937 0.00638 0.02682 0.32720 0.01788 0.66233 0.39317 0.19324 0.14388 0.88815 0.11568

0.00001 0.00000 0.00000 0.00000 0.01615 0.00001 0.00079 0.00114 0.00073 0.00009 0.00181 0.00258

0.00023 0.00000 0.00000 0.00001 0.99574 0.00002 0.00016 0.62893 0.44422 0.08819 0.00550 0.00217

0.00023 0.00300 0.00073 0.00246 0.03633 0.00000 0.00006 0.00186 0.00701 0.05501 0.00681 0.07943

0.34635 0.00566 0.00013 0.04742 0.06140 0.23874 0.47422 0.00199 0.00049 0.00200 0.00034 0.00377

0.00033 0.00000 0.00002 0.00113 0.13777 0.00018 0.00033 0.00903 0.00013 0.02596 0.50971 0.68541

0.00005 0.00000 0.00000 0.00000 0.06973 0.00101 0.01942 0.00379 0.00000 0.00155 0.00002 0.00106

0.00065 0.00006 0.00000 0.00000 0.08868 0.01284 0.00020 0.00651 0.00029 0.01598 0.00189 0.00002

0.01194 0.00000 0.00002 0.00003 0.17044 0.00483 0.10924 0.44459 0.01682 0.02277 0.00898 0.06250

0.00002 0.00000 0.26959 0.05098 0.01684 0.00007 0.01300 0.00426 0.00001 0.02859 0.06754 0.25395

0.00256 0.00035 0.00000 0.16351 0.11070 0.08404 0.03726 0.28511 0.00759 0.02680 0.00616 0.03823


0.00484 0.00019 0.21432 0.00024 0.03892 0.00005 0.00116 0.01364 0.00023 0.52935 0.00341 0.02149

0.00829 0.08535 0.90236 0.00001 0.16489 0.39100 0.00561 0.01016 0.00072 0.58034 0.01825 0.00202