Supplementary data S1. Accession numbers for the

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Abyssogena mariana. Abyssogena phaseoliformis. Akebiconcha kawamurai. Calyptogena fausta. Calyptogena laubieri. Calyptogena magnifica. Calyptogena ...
Supplementary data S1. Accession numbers for the vesicomyid DNA sequences used for phylogenetic analyses.

Species

Abyssogena mariana Abyssogena phaseoliformis Akebiconcha kawamurai Calyptogena fausta Calyptogena laubieri Calyptogena magnifica Calyptogena nautilei Calyptogena pacifica Isorropodon fossajaponicum Phreagena kilmeri Phreagena okutanii Phreagena soyoae Pliocardia stearnsii Meretrix lusoria Meretrix meretrix Meretrix petechialis Venerupis philippinarum Paphia euglypta

Mitochondrial genome sequence LC126311 AP014557 AP014551 AP014549 AP014553 KR862368 AP014554 AP014556 AP014550 AP014552 AP014555 AP014558 AP014559 NC_014809 NC_013188 NC_012767 NC_003354 NC_014579

Supplementary data S2. Accession numbers for the symbiont DNA sequences used for phylogenetic analyses. Symbiont gene sequence

Host species Abyssogena mariana

16S rRNA LC089762

23S rRNA LC089763

galU LC089858

groES-groEL LC089856

mfd LC089857

UvrA LC089859

UvrD paralog LC089860

Abyssogena phaseoliformis

AB479082

AB598132

LC090387

LC090398

AB911363

AB911373

AB911413

Akebiconcha kawamurai

AB479076

AB598138

LC090384

LC090393

AB911356

AB911366

AB911406

Calyptogena fausta

AB479081

AB598137

LC090382

LC090391

AB911359

AB911369

AB911409

Calyptogena laubieri

AB073121

AB598139

LC090385

LC090395

AB911357

AB911367

AB911407

Calyptogena magnifica

CP000488

CP000488

CP000488

CP000488

CP000488

CP000488

CP000488

Calyptogena nautilei

AB479080

AB598134

LC090389

LC090396

AB911361

AB911371

AB911411

Calyptogena pacifica

AF035723

AB598135

LC090386

LC090397

AB911362

AB911372

AB911412

Isorropodon fossajaponicum

AB044744

AB598133

LC225768

LC090392

AB911360

AB911370

AB911410

Phreagena kilmeri

AF035720

AB598136

LC090383

LC090394

AB911355

AB911365

AB911405

Phreagena okutanii

AP009247

AP009247

AP009247

AP009247

AP009247

AP009247

AP009247

Phreagena soyoae

AB479077

AB598140

LC090388

LC090399

AB911358

AB911368

AB911408

Pliocardia stearnsii

AB642238

AB642239

LC090390

LC090400

AB911364

AB911374

AB911414

Bathymodiolus septemdierum

AP013042

AP013042

AP013042

AP013042

AP013042

AP013042

AP013042

Supplementary data S3. Evolutionary models selected for the Maximum Likelihood (ML) and Bayesian analyses.

Partition Vesicomyid clam

atp6 atp8 cob cox1 cox2 cox3 nad1 nad3 nad4 nad5 rrnL Symbiont 16S rRNA 23S rRNA galU groEL groES mfd uvrA uvrD paralog

Maximum likelihood (ML)

GTR + G GTR + G GTR + G GTR + G GTR + G GTR + G GTR + G GTR + G GTR + G GTR + G GTR + G

GTR + G GTR + G GTR + G GTR + G GTR + G GTR + G GTR + G GTR + G

Bayesian analysis

HKY85 + G HKY85 + G HKY85 + G GTR + G GTR + G HKY85 + G HKY85 + G HKY85 + G GTR + G GTR + G GTR + G

HKY85 + G HKY85 + G HKY85 + G GTR + G GTR + G GTR + G GTR + G GTR + G

atp6

20/-

Abyssogena phaseoliformis

44/0.6176

71/0.9466

Abyssogena mariana

18/-

Pliocardia stearnsii

21/-

43/0.5610

11/-

Calyptogena nautilei

49/-

0.1

Calyptogena magnifica

40/-

Phreagena soyoae

99/0.9019

Phreagena kilmeri

82/0.9651

Phreagena okutanii Akebiconcha kawamurai 100/0.9862 Meretrix meretrix 100/1.0 Meretrix petechialis Meretrix lusoria 100/1.0 Paphia euglypta 95/0.9984 Venerupis philippinarum 100/1.0 Phreagena soyoae 97/1.0 Phreagena kilmeri

cob

63/0.8846

Phreagena okutanii

98/0.9996

0.1

20/0.5417

Venerupis philippinarum

cox1

Pliocardia stearnsii

31/0.5775

94/0.9978

Calyptogena nautilei Isorropodon fossajaponicum Abyssogena phaseoliformis

56/-

Abyssogena mariana

Calyptogena nautilei Meretrix meretrix 100/0.991 100/1.0 Meretrix petechialis Meretrix lusoria 100/1.0

100/0.9955

74/0.9805

Calyptogena pacifica 92/0.9851 Calyptogena fausta

Pliocardia stearnsii

100/0.9998

Calyptogena laubieri Calyptogena magnifica

59/0.9625

Abyssogena mariana

cox2

36/0.5029

72/0.9115

95/1.0

100/1.0

Phreagena okutanii Akebiconcha kawamurai

100/1.0

Abyssogena phaseoliformis

87/0.9985

Phreagena soyoae Phreagena kilmeri

11/-

cox3

100/0.9983 98/0.9966 78/0.9037

18/16/-

27/-

39/-

Phreagena okutanii Calyptogena pacifica

Calyptogena fausta

68/0.7694 0.1

Isorropodon fossajaponicum 100/0.9998

Phreagena soyoae Phreagena kilmeri

Akebiconcha kawamurai

50/0.8197 14/-

39/0.5443

Abyssogena phaseoliformis

21/-

90/0.9417

Abyssogena mariana

40/96/1.0

Pliocardia stearnsii

Calyptogena fausta

30/-

Abyssogena phaseoliformis Abyssogena mariana

Calyptogena magnifica

100/1.0

Calyptogena nautilei Calyptogena laubieri

31/-

Isorropodon fossajaponicum 28/-

100/1.0 88/0.9778

Pliocardia stearnsii

Calyptogena magnifica 96/0.9880 100/1.0

Meretrix meretrix Meretrix petechialis Meretrix lusoria

Calyptogena nautilei

Calyptogena laubieri

Akebiconcha kawamurai 98/0.9774 97/1.0

Venerupis philippinarum

Paphia euglypta

Calyptogena pacifica

94/0.9650

Meretrix petechialis

Meretrix lusoria Paphia euglypta

98/0.9999

Venerupis philippinarum

Meretrix meretrix

99/0.9963 100/1.0

100/1.0

Phreagena okutanii 0.1

Phreagena soyoae Phreagena kilmeri

100/1.0 100/1.0

100/1.0

100/1.0

Meretrix meretrix

Meretrix lusoria Meretrix petechialis Paphia euglypta

96/1.0

Calyptogena magnifica Calyptogena pacifica Calyptogena fausta

45/0.7407

58/0.6274 98/0.9970

85/0.9100

36/0.6152

Calyptogena laubieri Isorropodon fossajaponicum

27/0.7096

26/0.5163

0.1

Akebiconcha kawamurai

34/0.6937

Calyptogena nautilei Calyptogena pacifica

3/-

Calyptogena laubieri

100/1.0

2/-

Calyptogena laubieri Phreagena okutanii Akebiconcha kawamurai

Calyptogena fausta Pliocardia stearnsii Abyssogena phaseoliformis 5/48/0.8361 Abyssogena mariana 96/1.0 Calyptogena magnifica Isorropodon fossajaponicum

Isorropodon fossajaponicum

8/-

90/0.6992 Phreagena soyoae 50/0.7133 Phreagena kilmeri

99/0.9730

14/-

0.1

atp8

Calyptogena pacifica Calyptogena fausta

72/0.9472

Meretrix lusoria

96/1.0

Paphia euglypta Venerupis philippinarum

Meretrix meretrix Meretrix petechialis

100/1.0

Paphia euglypta Venerupis philippinarum

Supplementary data S4. Maximum likelihood (ML) phylogenies of 11 vesicomyid mitochondrial genes. Five venerid species (Meretrix lusoria, Meretrix meretrix, Meretrix petechialis, Paphia euglypta, and Venerupis philippinarum) served as an outgroup. Numbers at the bipartitions indicate the ML bootstrap supports (left) and Bayesian posterior probabilities (right). “-” indicates that the Bayesian tree did not recover the bipartition. Scale bars indicate the rate of internal nodes except for the outgroup. Orange boxes indicate the clades that include Akebiconcha kawamurai, Calyptogena laubieri, Phreagena kilmeri, Phreagena okutanii, and Phreagena soyoae. Green boxes indicate the clades that include Calyptogena fausta and Calyptogena pacifica. Blue boxes indicate the clades that include Abyssogena mariana and Abyssogena phaseoliformis.

nad1

nad3

100/1.0 Phreagena soyoae 96/0.9999 Phreagena kilmeri 92/0.9994 Phreagena okutanii

0.1

100/0.9998 34/0.5579

0.1

32/0.5085

Abyssogena mariana Calyptogena nautilei Isorropodon fossajaponicum

nad4

Isorropodon fossajaponicum

nad5

100/0.9993

Phreagena soyoae Phreagena kilmeri

98/0.9991

96/0.9937 91/0.9887

Phreagena okutanii

62/0.7817

Calyptogena laubieri

0.1

Calyptogena pacifica

73/0.9143

100/0.9981

36/0.8616

29/-

Calyptogena magnifica

100/1.0

Pliocardia stearnsii Calyptogena nautilei

Calyptogena pacifica Calyptogena fausta

23/-

Isorropodon fossajaponicum

38/-

petechialis

100/0.9999

Venerupis philippinarum

rrnL 100/0.9966 97/0.9679 71/0.8090

0.1

Phreagena kilmeri Phreagena okutanii Calyptogena laubieri Akebiconcha kawamurai

63/0.6545

Calyptogena pacifica

90/0.9790

Calyptogena fausta

65/0.8332

Abyssogena phaseoliformis

58/0.5775

100/1.0

94/0.9995

Abyssogena mariana

30/0.5068 48/0.8768

Isorropodon fossajaponicum

Calyptogena magnifica Pliocardia stearnsii Calyptogena nautilei

100/0.9967 100/1.0

Meretrix meretrix Meretrix petechialis Meretrix lusoria

100/1.0 100/1.0

Paphia euglypta Venerupis philippinarum

Supplementary data S4. Continued.

Meretrix meretrix Meretrix petechialis

Paphia euglypta Venerupis philippinarum

Phreagena soyoae

86/0.7936

98/0.9950 100/1.0

Meretrix lusoria

100/1.0

Paphia euglypta

99/1.0

Calyptogena nautilei

Abyssogena mariana

Meretrix lusoria

100/1.0

Pliocardia stearnsii

Abyssogena phaseoliformis

Meretrix meretrix

99/0.9245 100/1.0 Meretrix

Phreagena okutanii

Isorropodon fossajaponicum

0.1

Abyssogena mariana

Phreagena kilmeri

99/0.9968

39/-

Abyssogena phaseoliformis

Phreagena soyoae

Calyptogena magnifica

18/-

Calyptogena fausta

Paphia euglypta Venerupis philippinarum

100/1.0

Calyptogena laubieri

33/-

100/0.9999

59/0.9162

Meretrix lusoria

Akebiconcha kawamurai

96/0.9861

Akebiconcha kawamurai

82/0.8648

33/-

Abyssogena mariana

100/1.0 Meretrix lusoria Paphia euglypta Venerupis philippinarum

100/1.0

100/1.0

Abyssogena phaseoliformis

Pliocardia stearnsii Calyptogena magnifica 96/0.9125 Meretrix meretrix 100/1.0 Meretrix petechialis

100/0.9793 Meretrix meretrix 100/1.0 Meretrix petechialis

100/1.0

74/0.8910

Calyptogena nautilei

100/1.0

100/0.9996

100/1.0

Calyptogena fausta

30/0.5501

45/0.5593

Pliocardia stearnsii Calyptogena pacifica

Calyptogena fausta Calyptogena magnifica

Calyptogena pacifica

95/0.9991

64/0.5340

64/0.9779

100/1.0

Akebiconcha kawamurai

Calyptogena laubieri

8/-

53/0.5928

52/0.5645

Phreagena okutanii

32/-

62/0.6466

89/0.9999 29/-

50/0.5706 95/0.9948

Akebiconcha kawamurai Calyptogena laubieri Abyssogena phaseoliformis

Phreagena soyoae Phreagena kilmeri

99/0.9804

16S rRNA

23S rRNA

soyoae symbiont Phreagena kilmeri symbiont

98/0.9296 Phreagena 63/0.7010

0.1

100/1.0

Phreagena okutanii symbiont

0.1

99/0.9998 42/0.7335

Phreagena okutanii symbiont

100/1.0

67/0.7533

Calyptogena laubieri symbiont

26/-

Calyptogena laubieri symbiont

Calyptogena magnifica symbiont

31/-

Abyssogena mariana symbiont

Calyptogena pacifica symbiont

63/0.7889

67/0.9983

Pliocardia stearnsii symbiont

100/1.0 99/1.0

0.1

Phreagena kilmeri symbiont

Abyssogena phaseoliformis symbiont

Bathymodiolus septemdierum symbiont

groEL 0.1

Akebiconcha kawamurai symbiont

Akebiconcha kawamurai symbiont

50/0.5007

Calyptogena laubieri symbiont

Calyptogena laubieri symbiont

Calyptogena pacifica symbiont

Abyssogena mariana symbiont

96/0.9881

Isorropodon fossajaponicum symbiont

25/-

100/1.0

38/0.5201

Calyptogena nautilei symbiont

38/0.9014

Abyssogena phaseoliformis symbiont

Pliocardia stearnsii symbiont

50/0.8985

Abyssogena mariana symbiont

70/0.6229

Calyptogena nautilei symbiont

20/0.6952

Isorropodon fossajaponicum symbiont

68/0.8241

Calyptogena pacifica symbiont

63/0.6942

Calyptogena magnifica symbiont

35/-

Calyptogena fausta symbiont

0.1

Pliocardia stearnsii symbiont

63/0.9561

55/0.9585

Abyssogena phaseoliformis symbiont

groES

33/-

Calyptogena fausta symbiont

Calyptogena magnifica symbiont

100/1.0

Bathymodiolus septemdierum symbiont Phreagena kilmeri symbiont

Phreagena okutanii symbiont

Bathymodiolus septemdierum symbiont

mfd

100/1.0 33/0.6408

Akebiconcha kawamurai symbiont

40/0.7776

100/1.0 Phreagena soyoae symbiont 100/1.0 Phreagena kilmeri symbiont

0.1

100/1.0

Phreagena soyoae symbiont

27/-

Calyptogena laubieri symbiont 30/-

100/1.0

13/-

Isorropodon fossajaponicum symbiont

Calyptogena fausta symbiont

54/0.7262 100/1.0

Calyptogena nautilei symbiont

Calyptogena pacifica symbiont

Abyssogena phaseoliformis symbiont Calyptogena magnifica symbiont

Abyssogena mariana symbiont Bathymodiolus septemdierum symbiont

Phreagena okutanii symbiont Akebiconcha kawamurai symbiont

91/0.9705 53/0.7186

Calyptogena laubieri symbiont

Calyptogena pacifica symbiont

99/1.0

Pliocardia stearnsii symbiont

62/0.9409 60/0.5482 36/0.7044

Phreagena okutanii symbiont

100/1.0

74/0.5421 28/-

soyoae symbiont Phreagena kilmeri symbiont

100/0.9981 Phreagena 100/1.0

Phreagena okutanii symbiont

99/1.0

Calyptogena magnifica symbiont

45/0.5487

Bathymodiolus septemdierum symbiont Phreagena soyoae symbiont

Abyssogena mariana symbiont

Isorropodon fossajaponicum symbiont

54/0.5707

Abyssogena phaseoliformis symbiont

galU

Calyptogena nautilei symbiont

100/1.0

Calyptogena nautilei symbiont

65/0.9049

Pliocardia stearnsii symbiont

42/-

Calyptogena fausta symbiont

57/0.6472

Calyptogena fausta symbiont

96/1.0

Isorropodon fossajaponicum symbiont

100/1.0

Calyptogena pacifica symbiont

60/0.7204

100/1.0

65/0.8224 12/-

Phreagena kilmeri symbiont Akebiconcha kawamurai symbiont

75/0.9355

Akebiconcha kawamurai symbiont

Phreagena soyoae symbiont

100/1.0

Calyptogena fausta symbiont 88/0.9493 Pliocardia stearnsii symbiont 99/0.9998

Calyptogena nautilei symbiont Abyssogena mariana symbiont 100/1.0 Isorropodon fossajaponicum symbiont

51/0.6795

Calyptogena magnifica symbiont Abyssogena phaseoliformis symbiont

72/0.7786

Bathymodiolus septemdierum symbiont

Supplementary data S5. Maximum likelihood (ML) phylogenies of eight vesicomyid symbiont genes. The symbiont of the vent mussel Bathymodiolus septemdierum was used as an outgroup. Numbers at the bipartitions indicate ML bootstrap supports (left) and Bayesian posterior probabilities (right). “-” indicates that the Bayesian tree did not recover the bipartition. Scale bars indicate the rate of internal nodes, except for the outgroup Orange boxes indicate the clades that include the symbionts of Akebiconcha kawamurai, Calyptogena laubieri, Phreagena kilmeri, Phreagena okutanii, and Phreagena soyoae. Green boxes indicate the clades that include the symbionts of Calyptogena fausta, Calyptogena nautilei, Calyptogena pacifica, and Pliocardia stearnsii. Yellow boxes indicate the clades that include the symbionts of Abyssogena mariana and Isorropodon fossajaponicum.

uvrA

100/1.0 99/1.0

0.1

100/1.0

Phreagena kilmeri symbiont

Calyptogena laubieri symbiont

Calyptogena magnifica symbiont Abyssogena mariana symbiont

0.1

Abyssogena phaseoliformis symbiont Calyptogena pacifica symbiont

94/1.0

Calyptogena fausta symbiont

68/0.7411

Pliocardia stearnsii symbiont

100/1.0 100/1.0

Akebiconcha kawamurai symbiont Calyptogena laubieri symbiont Calyptogena magnifica symbiont

64/0.8799 93/0.9667

46/0.5318

Calyptogena pacifica symbiont Calyptogena fausta symbiont 100/1.0 Pliocardia stearnsii symbiont 56/0.7816 Calyptogena nautilei symbiont Abyssogena mariana symbiont 99/0.9995

99/0.9971

Isorropodon fossajaponicum symbiont

soyoae symbiont Phreagena kilmeri symbiont Phreagena okutanii symbiont

100/1.0 Phreagena

Phreagena okutanii symbiont

88/0.9050

56/0.8043

100/1.0

uvrD paralog

Akebiconcha kawamurai symbiont

80/0.9349

37/-

Phreagena soyoae symbiont

100/1.0

100/1.0

Isorropodon fossajaponicum symbiont Abyssogena phaseoliformis symbiont

100/1.0

97/0.9958

Calyptogena nautilei symbiont

Bathymodiolus septemdierum symbiont

Supplementary data S5. Continued.

Bathymodiolus septemdierum symbiont