Supporting information Table S1-S5

Invasions of an obligate asexual daphnid species support the nearly neutral theory

Hajime Ohtsuki1, Hirotomo Norimatsu1, Takashi Makino1 and Jotaro Urabe1*

Affiliations
1Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku,Sendai, 980-8578, Japan* Corresponding author: Jotaro Urabe (urabe@tohoku.ac.jp)

Table S1. Information on Daphnia pulex specimens analyzed in the present study.
SpeciesLineage

Genotype

LakeAreaNation

Latitude (°N)

Longitude (°E)

DDBJ Accesion number
Whole nuclear genome Whole mitocondorial genome

D. pulex

JPN1

AR01

Arigatani Ike

ShizuokaJapan

34.691138.126

SAMD00322344

LC632382

D. pulex

JPN1

DA04

Daizahoshi Ike

NaganoJapan

36.706138.145

SAMD00322345

LC632383

D. pulex

JPN1

DA05

Daizahoshi Ike

NaganoJapan

36.706138.145

SAMD00322346

LC632384

D. pulex

JPN1

FU01

Furuichi Oike

TottoriJapan

35.391133.339

SAMD00322347

LC632385

D. pulex

JPN1

HO03

Hataya Onuma

YamagataJapan

38.245140.204

SAMD00322348

LC632386

D. pulex

JPN1

KK01Kokenuma

YamagataJapan

38.231140.195

SAMD00322349

LC632387

D. pulex

JPN1

OS02

Osawa Tameike

MiyagiJapan

38.439140.919

SAMD00322350

LC632388

D. pulex

JPN2

AR05

Arigatani Ike

ShizuokaJapan

34.691138.126

SAMD00322351

LC632389

D. pulex

JPN2

HO01

Hataya Onuma

YamagataJapan

38.245140.204

SAMD00322352

LC632390

D. pulex

JPN2

PL2

Fukami Ike

NaganoJapan

35.326137.821

SAMD00322353

LC632391

D. pulex

JPN2

PL4

Fukami Ike

NaganoJapan

35.326137.821

SAMD00322354

LC632392

D. pulex

JPN2

PL7

Fukami Ike

NaganoJapan

35.326137.821

SAMD00322355

LC632393

D. pulex

JPN3

AWA

Awaji Nariai-ji

Hyogo

Japan

34.283134.809

SAMD00322356

LC632394

D. pulex

JPN4

SUM

Sumiyoshi Ike

KagoshimaJapan

31.772130.592

SAMD00322357

LC632395

PUC01

Lake Biwa

Shiga

Japan

35.191135.994

SAMD00322358-

D. pulicaria

E5

a small lake

NYUSA

SAMD00322359-

D. pulex

NoE14

a small lake

NYUSA

SAMD00322360-

D. pulex

LL05

a small lake

Manitoba

Canada

SAMD00322361-D. pulicaria

Table S2. Substitution rates and estimated divergence times for each lineage

Avg. subst.
rate

Div.time(3gen/yr)

Div.time(5en/yr)

Div.time(10gen/yr)

TCO

1.07E-05

848

509

254

PA42

1.82E-05

499

299

150

TCO

9.00E-06

621

373

186

PA42

1.34E-05

416

250

125

Lineage

Reference

JPN1JPN2

Table S3. The numbers of nonsynonymous and synonymous substitutions and that in noncoding regions estimated by the pairwise comparisons between genotypes within JPN1 andJPN2 lineages, and results of t-test examining the difference between these lineages
Nonsynonymous

Synonymous

Non-coding(ΔNsy )(ΔSyn )

(Δnon-C )AR01vsDA04

2925694275

AR01vsDA05

309

593

4757

AR01vsFU01

305

574

4900

AR01vsHO03

283

541

4168

AR01vsKK01

297

604

4403

AR01vsOS02

280

544

4153

DA04vsDA05

295

514

4016

DA04vsFU01

289

491

3901

DA04vsHO03

289

492

4115

DA04vsKK01

293

561

4176

DA04vsOS02

276

533

4062

DA05vsFU01

240

413

3253

DA05vsHO03

276

536

4305

DA05vsKK01

2945354144

DA05vsOS02

2875574358

FU01vsHO03

2585074338

FU01vsKK01

260

5104145

FU01vsOS02281

512

4349

HO03vsKK01274531

4211

HO03vsOS02253

479

4067

KK01vsOS02287536

4154

AR05vsHO01254

4843074

AR05vsPL2

229

445

2867

AR05vsPL4

243

433

2770

AR05vsPL7

292

493

3234

HO01vsPL2

239

417

2619

HO01vsPL4

235

433

2736

HO01vsPL7

304

515

3466

PL2vsPL4

202

382

2465

PL2vsPL7

271

480

3243

PL4vsPL7

283

478

3162

Lineage

Pair

JPN1

JPN2

t-test exaining statistical difference begtween JPN1 and JPN2 lineages
t -value

3.582

6.445

29.540p -value> 0.05

< 0.001< 0.001

Table S4. List of genes with unique nonsynonymous substitutions in eachgenotype.
Data are listed in the order corresponding to gene stable IDs of TCO(Colbourne et al. 2012). Filled and open circles denote homozygous andheterozygous mutations on the gene, respectively.

JPN1Gene stable ID

JPN2

AR0DA0DA0FU0HO0KK0OS0AR0HO0PL

PLPL

145131251247○

DAPPUDRAFT_100142
DAPPUDRAFT_100184○DAPPUDRAFT_100200●○DAPPUDRAFT_101046○DAPPUDRAFT_101087
DAPPUDRAFT_102050●○DAPPUDRAFT_102106
DAPPUDRAFT_102133●

DAPPUDRAFT_102173●

DAPPUDRAFT_102448●○DAPPUDRAFT_102589●

DAPPUDRAFT_102606
DAPPUDRAFT_102698○○

DAPPUDRAFT_103010●

DAPPUDRAFT_103833○

DAPPUDRAFT_104592
DAPPUDRAFT_104787○○

DAPPUDRAFT_104885○

DAPPUDRAFT_105173○○

DAPPUDRAFT_105768
DAPPUDRAFT_106149○

DAPPUDRAFT_106477●

DAPPUDRAFT_106666●○

DAPPUDRAFT_106883
DAPPUDRAFT_106899○●

○

DAPPUDRAFT_107340●

DAPPUDRAFT_107700○

DAPPUDRAFT_108150○

DAPPUDRAFT_108326
DAPPUDRAFT_108478○

DAPPUDRAFT_109031○●

DAPPUDRAFT_109282○

DAPPUDRAFT_109456○○

DAPPUDRAFT_109764○

DAPPUDRAFT_109956○

DAPPUDRAFT_110077○

DAPPUDRAFT_110200○

DAPPUDRAFT_110341
DAPPUDRAFT_110847○

DAPPUDRAFT_111210○

DAPPUDRAFT_111549●○

DAPPUDRAFT_113018●

DAPPUDRAFT_113547○

DAPPUDRAFT_113947
DAPPUDRAFT_114229●○

DAPPUDRAFT_114231●

DAPPUDRAFT_114273○

DAPPUDRAFT_114320○

DAPPUDRAFT_114421○

DAPPUDRAFT_114604○

DAPPUDRAFT_114926●

DAPPUDRAFT_116883●DAPPUDRAFT_116884●

DAPPUDRAFT_117019
DAPPUDRAFT_117545○○

DAPPUDRAFT_117736
DAPPUDRAFT_117737
DAPPUDRAFT_117879○○○●

DAPPUDRAFT_119275
DAPPUDRAFT_119531○○

DAPPUDRAFT_120478○

DAPPUDRAFT_120630●

DAPPUDRAFT_123888
DAPPUDRAFT_124162○○

DAPPUDRAFT_127260○

DAPPUDRAFT_1338○

DAPPUDRAFT_186887○

DAPPUDRAFT_188071
DAPPUDRAFT_194168●

DAPPUDRAFT_194355○○

DAPPUDRAFT_196016●

DAPPUDRAFT_197829○

DAPPUDRAFT_199479○

DAPPUDRAFT_200371
DAPPUDRAFT_200491○

DAPPUDRAFT_201971○●

DAPPUDRAFT_204745○

DAPPUDRAFT_208272○

DAPPUDRAFT_210457○

DAPPUDRAFT_213335○

DAPPUDRAFT_214350
DAPPUDRAFT_218706○

DAPPUDRAFT_218819○○

DAPPUDRAFT_220911○

DAPPUDRAFT_221352●

DAPPUDRAFT_221821●

DAPPUDRAFT_222068○

DAPPUDRAFT_222344○

DAPPUDRAFT_223107
DAPPUDRAFT_223110○●

DAPPUDRAFT_224080○

DAPPUDRAFT_226467
DAPPUDRAFT_227934●

DAPPUDRAFT_228516○

DAPPUDRAFT_228726

○

○

●

DAPPUDRAFT_231325○

DAPPUDRAFT_231992○

DAPPUDRAFT_234464
DAPPUDRAFT_234592○○

DAPPUDRAFT_235227○

DAPPUDRAFT_235623●

DAPPUDRAFT_235675
DAPPUDRAFT_235814●

DAPPUDRAFT_236078○○

DAPPUDRAFT_236114○

DAPPUDRAFT_236160○

DAPPUDRAFT_237497○

DAPPUDRAFT_237515●●

DAPPUDRAFT_238573○

DAPPUDRAFT_238928●

DAPPUDRAFT_238989○

DAPPUDRAFT_239551○

DAPPUDRAFT_239781○○

DAPPUDRAFT_239901
DAPPUDRAFT_240350●

DAPPUDRAFT_240561○○

DAPPUDRAFT_240676●

DAPPUDRAFT_241840○

DAPPUDRAFT_242342
DAPPUDRAFT_242810○

DAPPUDRAFT_244506○○

DAPPUDRAFT_244635
DAPPUDRAFT_246189●

DAPPUDRAFT_246435○

DAPPUDRAFT_246486
DAPPUDRAFT_247464○●

DAPPUDRAFT_247774
DAPPUDRAFT_248360
DAPPUDRAFT_249918
DAPPUDRAFT_250461

○○○

●

DAPPUDRAFT_251296○

DAPPUDRAFT_251607
DAPPUDRAFT_251710○●○

DAPPUDRAFT_251767●

DAPPUDRAFT_253359●

DAPPUDRAFT_253382○

DAPPUDRAFT_253578○

DAPPUDRAFT_253899●

DAPPUDRAFT_254022●

DAPPUDRAFT_254610○

DAPPUDRAFT_256362
DAPPUDRAFT_258674●○○

DAPPUDRAFT_259829○

DAPPUDRAFT_259872○DAPPUDRAFT_260043○

DAPPUDRAFT_260396○

DAPPUDRAFT_260662
DAPPUDRAFT_262014○

DAPPUDRAFT_262510○

DAPPUDRAFT_263269○

DAPPUDRAFT_263370●○

DAPPUDRAFT_263616○○

DAPPUDRAFT_263869○

DAPPUDRAFT_264458○

DAPPUDRAFT_264791●

DAPPUDRAFT_264813○

DAPPUDRAFT_265215●

DAPPUDRAFT_265372
DAPPUDRAFT_265628○○○

DAPPUDRAFT_265983●

DAPPUDRAFT_266275
DAPPUDRAFT_266638○○

DAPPUDRAFT_271148○

DAPPUDRAFT_299651○

DAPPUDRAFT_299927○●DAPPUDRAFT_300404○

DAPPUDRAFT_300508○

DAPPUDRAFT_301167○

DAPPUDRAFT_301201○

DAPPUDRAFT_301407○

DAPPUDRAFT_301532●

DAPPUDRAFT_301877○

DAPPUDRAFT_301897○

DAPPUDRAFT_302117○

DAPPUDRAFT_302134○

DAPPUDRAFT_302138●

DAPPUDRAFT_302484○

DAPPUDRAFT_302612○

DAPPUDRAFT_302657
DAPPUDRAFT_302833●

DAPPUDRAFT_302844○

DAPPUDRAFT_302885○

DAPPUDRAFT_303105●

DAPPUDRAFT_303198●○

DAPPUDRAFT_303205○

DAPPUDRAFT_303246●○

DAPPUDRAFT_303405○

DAPPUDRAFT_303483
DAPPUDRAFT_303885○

DAPPUDRAFT_303904○DAPPUDRAFT_303927○●

DAPPUDRAFT_304023
DAPPUDRAFT_304124○○○

DAPPUDRAFT_304125○

DAPPUDRAFT_304131○

DAPPUDRAFT_304382○

DAPPUDRAFT_304684
DAPPUDRAFT_304801○

DAPPUDRAFT_304875
DAPPUDRAFT_304939○DAPPUDRAFT_304943●DAPPUDRAFT_305286○

DAPPUDRAFT_30529

○

○

○

DAPPUDRAFT_305332○

DAPPUDRAFT_305389
DAPPUDRAFT_305668○

DAPPUDRAFT_305909○○○

DAPPUDRAFT_306244○

DAPPUDRAFT_306421
DAPPUDRAFT_30674○

DAPPUDRAFT_306779○○●DAPPUDRAFT_306814○

DAPPUDRAFT_306924○

DAPPUDRAFT_307384○

DAPPUDRAFT_307822
DAPPUDRAFT_307855○

DAPPUDRAFT_308050
DAPPUDRAFT_308560○○

DAPPUDRAFT_308709○

DAPPUDRAFT_308845○

DAPPUDRAFT_308901○

DAPPUDRAFT_30917○

DAPPUDRAFT_309233○

DAPPUDRAFT_309396○

DAPPUDRAFT_309401●DAPPUDRAFT_309961○

DAPPUDRAFT_310325
DAPPUDRAFT_310536○

DAPPUDRAFT_310578○

DAPPUDRAFT_311177○○

DAPPUDRAFT_311292●DAPPUDRAFT_311786
DAPPUDRAFT_311898○

DAPPUDRAFT_312544○

DAPPUDRAFT_313288○○DAPPUDRAFT_313504
DAPPUDRAFT_313554●

DAPPUDRAFT_314003○

DAPPUDRAFT_314497●○

DAPPUDRAFT_314878○

DAPPUDRAFT_315894○

DAPPUDRAFT_316279
DAPPUDRAFT_316320○

DAPPUDRAFT_316647○

DAPPUDRAFT_317276○

DAPPUDRAFT_317513○

DAPPUDRAFT_318035
DAPPUDRAFT_318220○○

DAPPUDRAFT_318416
DAPPUDRAFT_318862○

DAPPUDRAFT_319139○○

DAPPUDRAFT_319198
DAPPUDRAFT_319275○○

DAPPUDRAFT_319459●○

DAPPUDRAFT_319496
DAPPUDRAFT_319819●

DAPPUDRAFT_319936○●○DAPPUDRAFT_320142○

DAPPUDRAFT_320244●

DAPPUDRAFT_321105
DAPPUDRAFT_322033○○○

DAPPUDRAFT_322293
DAPPUDRAFT_323470○○

DAPPUDRAFT_323689
DAPPUDRAFT_323811○

DAPPUDRAFT_324583○

DAPPUDRAFT_324745○○

DAPPUDRAFT_325092
DAPPUDRAFT_325573○

DAPPUDRAFT_325621○

○

DAPPUDRAFT_325795●

DAPPUDRAFT_325898○

DAPPUDRAFT_326717○

DAPPUDRAFT_326941○

DAPPUDRAFT_326957○

DAPPUDRAFT_327022●DAPPUDRAFT_327679
DAPPUDRAFT_328037○○

DAPPUDRAFT_328318●DAPPUDRAFT_328712○

DAPPUDRAFT_329106○

DAPPUDRAFT_329385○

DAPPUDRAFT_329664○●

DAPPUDRAFT_329805
DAPPUDRAFT_329962○

DAPPUDRAFT_330286●○

DAPPUDRAFT_330570●

DAPPUDRAFT_330625○

DAPPUDRAFT_330844○

DAPPUDRAFT_330970○

DAPPUDRAFT_331526
DAPPUDRAFT_331838●

DAPPUDRAFT_332703○○

DAPPUDRAFT_332853○○

DAPPUDRAFT_333387○

DAPPUDRAFT_333581○

DAPPUDRAFT_333653○

DAPPUDRAFT_333828○

DAPPUDRAFT_334025○

DAPPUDRAFT_334105
DAPPUDRAFT_334794●○

DAPPUDRAFT_335346
DAPPUDRAFT_335601○○

DAPPUDRAFT_33293
DAPPUDRAFT_332948○●

○

DAPPUDRAFT_335789○

DAPPUDRAFT_340525●

DAPPUDRAFT_340854○

DAPPUDRAFT_346846
DAPPUDRAFT_346847●

DAPPUDRAFT_347258○●

DAPPUDRAFT_347585○

DAPPUDRAFT_347609
DAPPUDRAFT_40007●●○

DAPPUDRAFT_40651●

DAPPUDRAFT_41180○

DAPPUDRAFT_41292●

DAPPUDRAFT_42306●

DAPPUDRAFT_42461●○

DAPPUDRAFT_442477●

DAPPUDRAFT_45783○

DAPPUDRAFT_47834○○DAPPUDRAFT_52115○○

DAPPUDRAFT_52511○

DAPPUDRAFT_55188○

DAPPUDRAFT_58148●

DAPPUDRAFT_58385○

DAPPUDRAFT_58979○

DAPPUDRAFT_59583○

DAPPUDRAFT_59739○

DAPPUDRAFT_60562●

DAPPUDRAFT_60927○

DAPPUDRAFT_62213
DAPPUDRAFT_64710○

DAPPUDRAFT_65729●

DAPPUDRAFT_7338○

DAPPUDRAFT_93942○

DAPPUDRAFT_94669
DAPPUDRAFT_94746
DAPPUDRAFT_95082

○○○

○

DAPPUDRAFT_97099○

DAPPUDRAFT_97244○

DAPPUDRAFT_97326○

DAPPUDRAFT_97672○

DAPPUDRAFT_98367
DAPPUDRAFT_99493
DAPPUDRAFT_99701
DAPPUDRAFT_99799○●○

Table S5. List of primers for sequencing whole genome DNA. Names of primer used for
amplifying each region (set 1, 2 and 3) are shown in bold.

name
Set 1

Dpu_01488F1

Dpu_02163F1
Dpu_02863F1
Dpu_03521F1
Dpu_04918R1
Dpu_05556R1
Dpu_06200R1
Set 2

Dpu_06899R1
Dpu_06487F2

Dpu_07124F2
Dpu_07650F2
Dpu_07822F2
Dpu_08126F2
Dpu_08436R2
Dpu_08641F2
Dpu_09209F2
Dpu_09729F2
Dpu_10758R2
Dpu_11130R2Dpu_11445R2
Dpu_12035R2
Dpu_12336R2
Dpu_12606R2
Dpu_12761R2
Dpu_13323R2
Dpu_13787R2
Set 3

Dpu_14188R2
Dpu_13944F3

Dpu_14626F3
Dpu_14685F3
Dpu_00747R3
Dpu_01182R3
Dpu_01385R3
Dpu_02003R3

sequence
GCTCTTAGACTTTTAATTCGCGCCG
ATTATTAGCCACGAAAGAGGCTTCAATCGAATGACAGCATTCACGCCGTACCTGGTCGTTTAAATCGAGGCAATGAACAAGATTATTCCCCAAGACCACAGATCTAATTGTCTCAATGATTTGAGAACAGCT
GCCTTTCTTAGCGGGGTTTTACTCTAACCTCTAAACTTCCTAACTGCCCCTCTAAGGGTAGACAATGCAAGATAGCCATAGAAGCAACAATTCTCCCCCCTAAAAATCACTCCTGTCTGTTCAATGTTGGGTAGACATTAGTCACGGCCTCTGTTCAGGGACAACTCGAACTATTCCG
AGGCCTAATCCAAACCCGCTTAACACCCAAAGCTCCCAAAGCTCCA
GGGATAGCAGAGAGTAAATTGG
CTTCTACAGGCTTTGCTCCGATTCTAGGTTAAACAATCTTATGC
TTGGATGTCTACGAGGAGTAGCCCATACATTCAGTTGCGTAAGGGGCAGCCAGGTTGGTTTCTATCCTCCTAGGGATAACAGCGTAATCGTGTTTATCTATCTACCAGAATACCCATCTTTGTCCAAATTGTG
AGGCTTAAAACTCAGGTGAAGGTGG
TTGAGAAGAGAGTGACGGGCGATATAGCCAGATTCAAACTTTCCCCGGAACCACTTTAGCGCAAGTA
CTGTCATCAACCAGCCTACATGGAAAGTAGATCATGGATAGC
ATGGCCGAGGAGTAGGCATTAATGCTAGGACTGGTAGGCTCAATAG