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Table 1 Samples used in this study.

From: Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries

Sample information

   

GenBank Accession Number

Laboratory sample number

Field Identification

Locality

Voucher localisation

Phylogenetic species

Cyt b

COI

IRBP

MDZ10Mada

Rattus rattus

Madagascar

 

R1

HM217368

HM217495

HM217603

ratcosT820

Rattus rattus

India

 

R1

HM217367

HM217498

HM217606

ratcosR12

Rattus rattus

Oman

 

R1

HM217366

HM217496

HM217604

ratcosTE4264

Rattus rattus

Tanzania

 

R1

HM217365

HM217497

HM217605

R4003

Rattus tanezumi

Kalasin (Thailand)

MahaU

R2

HM217436

HM217563

HM217673

R2953

Rattus tanezumi

Kanchanaburi (Thailand)

 

R7

HM217396

HM217525

HM217634

R2996

Rattus tanezumi

Kanchanaburi (Thailand)

 

R2

HM217398

HM217529

HM217636

R3122

Rattus tanezumi

Kanchanaburi (Thailand)

 

R2

HM217407

HM217537

HM217645

R3214

Rattus tanezumi

Kanchanaburi (Thailand)

 

R2

HM217410

HM217540

HM217648

R3573

Rattus tanezumi

Nakhon Pathom (Thailand)

KU

R2

HM217430

HM217558

HM217667

R4016

Rattus tanezumi

Phrae (Thailand)

CBGP

R2

HM217438

HM217565

HM217675

R4424

Rattus tanezumi

Phrae (Thailand)

MahaU

R2

HM217456

HM217582

HM217693

R4436

Rattus tanezumi

Phrae (Thailand)

MahaU

R2

HM217457

HM217583

HM217694

R5294

Rattus tanezumi

Nan (Thailand)

MahaU

R2

HM217466

HM217592

HM217704

R5296

Rattus tanezumi

Nan (Thailand)

CBGP

R2

HM217467

HM217593

HM217705

L0100

Rattus tanezumi

Luang Prabang (LPDR)

MahaU

R2

HM217475

HM217489

HM217712

L0194

Rattus tanezumi

Luang Prabang (LPDR)

MahaU

R2

HM217480

HM217494

HM217717

R3029

Rattus tanezumi

Bangkok (Thailand)

 

R3

HM217399

HM217530

HM217637

R1843

Rattus tanezumi

Krabi (Thailand)

 

R3

HM217393

HM217524

HM217631

R1147

Rattus tanezumi

Nakhon Ratchasima (Thailand)

 

R3

HM217384

HM217515

HM217622

R1016

Rattus tanezumi

Nakhon Ratchasima (Thailand)

 

R3

HM217382

HM217513

HM217620

R1818

Rattus tanezumi

Prachinburi (Thailand)

 

R3

HM217389

HM217520

HM217627

R2794

Rattus tanezumi

Ratchaburi (Thailand)

 

R3

HM217394

HM217526

HM217632

R0169

Rattus tanezumi

Ratchaburi (Thailand)

 

R3

HM217372

HM217503

HM217610

CB0028

Rattus tanezumi

Veal Renh (Cambodia)

MahaU

R3

HM217363

HM217485

HM217601

R1833

Rattus tanezumi

Nakhon Sri Thammarat (Thailand)

 

R5

HM217391

HM217522

HM217629

R4402

Rattus losea

Loei (Thailand)

MahaU

R4

HM217454

HM217581

HM217691

R3484

Rattus losea

Loei (Thailand)

 

R4

HM217421

HM217550

HM217659

R4230

Rattus losea

Loei (Thailand)

CBGP

R4

HM217446

HM217573

HM217683

R1015

Rattus losea

Nakhon Ratchasima (Thailand)

 

R4

HM217381

HM217512

HM217619

R4203

Rattus losea

Phrae (Thailand)

CBGP

R4

HM217443

HM217570

HM217680

R3510

Rattus losea

Phrae (Thailand)

 

R4

HM217423

HM217552

HM217661

R0237

Rattus losea

Ratchaburi (Thailand)

 

R4

HM217374

HM217505

HM217612

R0238

Rattus losea

Ratchaburi (Thailand)

 

R4

HM217375

HM217506

HM217613

R1805

Rattus exulans

Bangkok (Thailand)

 

R8

HM217388

HM217519

HM217626

R4004

Rattus exulans

Kalasin (Thailand)

MahaU

R8

HM217437

HM217564

HM217674

R3224

Rattus exulans

Kanchanaburi (Thailand)

 

R8

HM217411

HM217541

HM217649

R4103

Rattus exulans

Loei (Thailand)

MahaU

R8

HM217440

HM217567

HM217677

R1055

Rattus exulans

Nakhon Ratchasima (Thailand)

 

R8

HM217383

HM217514

HM217621

R1836

Rattus exulans

Nakhon Sri Thammarat (Thailand)

 

R8

HM217392

HM217523

HM217630

R4140

Rattus exulans

Phrae (Thailand)

MahaU

R8

HM217441

HM217568

HM217678

R0284

Rattus exulans

Ratchaburi (Thailand)

 

R8

HM217377

HM217508

HM217615

R2795

Rattus exulans

Ratchaburi (Thailand)

 

R8

HM217395

HM217527

HM217633

R3520

Rattus exulans

Sakhon Nakhon (Thailand)

MahiU

R8

HM217424

HM217553

HM217662

R3563

Rattus exulans

Surat Thani (Thailand)

KU

R8

HM217428

HM217557

HM217666

R5349

Rattus exulans

Nan (Thailand)

CBGP

R8

HM217470

HM217595

HM217703

R5447

Rattus exulans

Nan (Thailand)

CBGP

R8

HM217472

HM217596

HM217708

CB0001

Rattus argentiventer

Veal Renh (Cambodia)

MahaU

R6

HM217362

HM217484

HM217600

CB0104

Rattus argentiventer

Veal Renh (Cambodia)

MahaU

R6

HM217364

HM217486

HM217602

R3087

Rattus andamanensis

Kanchanaburi (Thailand)

 

R7

HM217403

HM217533

HM217641

R4377

Rattus andamanensis

Loei (Thailand)

MahaU

R2

HM217452

HM217579

HM217689

R3548

Rattus andamanensis

Phrae (Thailand)

KU

R2

HM217426

HM217555

HM217664

R4481

Rattus andamanensis

Phrae (Thailand)

MahaU

R2

HM217458

HM217584

HM217695

R0130

Rattus andamanensis

Ratchaburi (Thailand)

 

R2

HM217371

HM217502

HM217608

R2976

Rattus andamanensis

Nakhon Pathom (Thailand)

 

R3

HM217397

HM217528

HM217635

R3565

Rattus norvegicus

Nakhon Pathom (Thailand)

MahiU

R9

HM217429

-

-

R0223

Rattus norvegicus

Ratchaburi (Thailand)

 

R9

HM217373

HM217504

HM217611

R0115

Rattus norvegicus

Ratchaburi (Thailand)

 

R9

HM217370

HM217501

HM217609

RNO 032

Rattus norvegicus

Cambodia

 

R9

HM217481

HM217499

-

L0180

Rattus nitidus

Luang Prabang (LPDR)

MahaU

R10

HM217478

HM217492

HM217715

L0192

Rattus nitidus

Luang Prabang (LPDR)

MahaU

R10

HM217479

HM217493

HM217716

R4188

Rattus sp.

Phrae (Thailand)

CBGP

R3

HM217442

HM217569

HM217679

L0010

Rattus sp.

Luang Prabang (LPDR)

MahaU

R10

HM217474

HM217488

HM217711

R0856

Bandicota indica

Nakhon Pathom (Thailand)

 

R8

HM217379

HM217510

HM217617

R4001

Bandicota indica

Kalasin (Thailand)

MahaU

B1

HM217435

-

HM217672

R3189

Bandicota indica

Kanchanaburi (Thailand)

 

B1

HM217408

HM217538

HM217646

R4265

Bandicota indica

Loei (Thailand)

CBGP

B1

HM217447

HM217574

HM217684

R1006

Bandicota indica

Nakhon Ratchasima (Thailand)

 

B1

HM217380

HM217511

HM217618

R3521

Bandicota indica

Phrae (Thailand)

KU

B1

HM217425

HM217554

HM217663

R0269

Bandicota indica

Ratchaburi (Thailand)

 

B1

HM217376

HM217507

HM217614

R0304

Bandicota indica

Ratchaburi (Thailand)

 

B1

HM217378

HM217509

HM217616

R5313

Bandicota indica

Nan (Thailand)

MahaU

B1

HM217469

HM217594

HM217706

L0142

Bandicota indica

Luang Prabang (LPDR)

MahaU

B1

HM217476

HM217490

HM217713

R4408

Bandicota indica

Loei (Thailand)

CBGP

B2

HM217455

-

HM217692

R1284

Bandicota savilei

Nakhon Ratchasima (Thailand)

 

B1

HM217386

HM217517

HM217624

R1822

Bandicota savilei

Nakhon Pathom (Thailand)

 

B1

HM217390

HM217521

HM217628

R1797

Bandicota savilei

Kanchanaburi (Thailand)

 

B2

HM217387

HM217518

HM217625

R1191

Bandicota savilei

Nakhon Ratchasima (Thailand)

 

B2

HM217385

HM217516

HM217623

R3550

Bandicota savilei

Phrae (Thailand)

KU

B2

HM217427

HM217556

HM217665

R0093

Bandicota sp.

Ratchaburi (Thailand)

 

B2

HM217369

HM217500

HM217607

R3050

Berylmys berdmorei

Kanchanaburi (Thailand)

 

Be1

HM217401

HM217532

HM217639

R4266

Berylmys berdmorei

Loei (Thailand)

CBGP

Be1

HM217448

HM217575

HM217685

R3441

Berylmys berdmorei

Loei (Thailand)

MahiU

Be1

HM217418

HM217547

HM217656

R5310

Berylmys berdmorei

Nan (Thailand)

MahaU

Be1

HM217468

-

HM217709

L0006

Berylmys berdmorei

Luang Prabang (LPDR)

MahaU

Be1

HM217473

HM217487

HM217710

R3618

Berylmys berdmorei

Phrae (Thailand)

KU

Be1

HM217432

HM217560

HM217669

R3603

Berylmys berdmorei

Phrae (Thailand)

KU

Be1

HM217431

HM217559

HM217668

R4400

Berylmys bowersi

Loei (Thailand)

MahaU

Be2, a

HM217453

HM217580

HM217690

R3425

Berylmys bowersi

Loei (Thailand)

KU

Be2, a

HM217415

HM217544

HM217653

R3415

Berylmys bowersi

Loei (Thailand)

KU

Be2, a

HM217413

HM217542

HM217651

R5410

Berylmys bowersi

Nan (Thailand)

MahaU

Be2, a

HM217471

-

HM217707

L0151

Berylmys bowersi

Luang Prabang (LPDR)

MahaU

Be2, a

HM217477

HM217491

HM217714

R3268

Berylmys bowersi

Kanchanaburi (Thailand)

KU

Be2, b

HM217412

HM217597

HM217650

R4098

Leopoldamys sabanus

Loei (Thailand)

CBGP

L1

HM217439

HM217566

HM217676

R4222

Leopoldamys sabanus

Loei (Thailand)

MahaU

L1

HM217444

HM217571

HM217681

R4296

Leopoldamys sabanus

Phrae (Thailand)

MahaU

L1

HM217450

HM217577

HM217687

R4276

Leopoldamys sabanus

Phrae (Thailand)

CBGP

L1

HM217449

HM217576

HM217686

R4370

Leopoldamys sabanus

Phrae (Thailand)

CBGP

L1

HM217451

HM217578

HM217688

R3111

Leopoldamys sabanus

Kanchanaburi (Thailand)

 

L3

HM217404

HM217534

HM217642

R3033

Leopoldamys sabanus

Kanchanaburi (Thailand)

 

L3

HM217400

HM217531

HM217638

R4517

Leopoldamys neilli

Loei (Thailand)

MahaU

L2

HM217462

HM217588

HM217699

R4527

Leopoldamys neilli

Loei (Thailand)

MahaU

L2

HM217463

HM217590

HM217701

R4486

Leopoldamys neilli

Phrae (Thailand)

MahaU

L2

HM217460

HM217586

HM217697

R4485

Leopoldamys neilli

Phrae (Thailand)

MahaU

L2

HM217459

HM217585

HM217696

R3419

Leopoldamys sp.

Loei (Thailand)

KU

L1

HM217414

HM217543

HM217652

R4723

Niviventer fulvescens

Loei (Thailand)

MahaU

N1

HM217465

HM217591

HM217702

R3212

Niviventer fulvescens

Kanchanaburi (Thailand)

KU

N2

HM217409

HM217539

HM217647

R4525

Niviventer sp.

Loei (Thailand)

MahaU

N1

HM217464

HM217589

HM217700

R3427

Niviventer sp.

Loei (Thailand)

KU

N1

HM217416

HM217545

HM217654

R3429

Niviventer sp.

Loei (Thailand)

KU

N1

HM217417

HM217546

HM217655

R3459

Niviventer sp.

Loei (Thailand)

KU

N1

HM217419

HM217548

HM217657

R4497

Niviventer sp.

Phrae (Thailand)

MahaU

N1

HM217461

HM217587

HM217698

R3492

Niviventer sp.

Loei (Thailand)

KU

N1

HM217422

HM217551

HM217660

R3077

Niviventer sp.

Kanchanaburi (Thailand)

MahiU

N3

HM217402

-

HM217640

R3795

Nu Deng*

Khammouane (LPDR)

MahiU

N4

HM217433

HM217561

HM217670

R3796

Nu Deng*

Khammouane (LPDR)

MahiU

N4

HM217434

HM217562

HM217671

R3118

Maxomys surifer

Kanchanaburi (Thailand)

 

M1

HM217406

HM217536

HM217644

R3116

Maxomys surifer

Kanchanaburi (Thailand)

 

M1

HM217405

HM217535

HM217643

R4223

Maxomys surifer

Loei (Thailand)

CBGP

M2

HM217445

HM217572

HM217682

R3464

Maxomys surifer

Loei (Thailand)

KU

M2

HM217420

HM217549

HM217658

MK0509 BZ02

Micromys minutus

China

CBGP

Outgroup

HM217360

HM217482

HM217598

MK0509 BZ07

Micromys minutus

China

CBGP

Outgroup

HM217361

HM217483

HM217599

  1. Field identifications were achieved based on morphological criteria according to [33–35] and [11].
  2. "Phylogenetic species" relies on the DNA-based species delimitation method (see also Figure 3).
  3. Mismatches between field identifications and phylogenetic species are highlighted in bold and reflect the difficulty to identify rat species even for experts.
  4. "Nu deng*" was assigned to animal identified but impossible to assigned to a particular species; in Thai language, "red rat".
  5. "-" corresponds to missing data in the phylogenetic analyses.
  6. Voucher locations:
  7. CBGP: Centre de Biologie et de Gestion des Populations, Montpellier, France - curator of the collections, Y. Chaval, chaval@supagro.inra.fr/KU: Kasetsart University, Bangkok, Thailand - curator: W. Rerkamnuaychoke/MahiU: Mahidol University, Nakhon Pathom, Thailand - curator: V. Herbreteau, vincent.herbreteau@cirad.fr/MahaU: Mahasarakham University, Mahasarakham, Thailand - curator: S. Soonchan
  8. See Figure 1 for additional information about sample locations.