Appendix S1 List of specimens used in this study including

Appendix S1 List of specimens used in this study including sampling date and location and GenBank accession numbers
Sample ID
DNA
RNA
23H8
23H9
23I1
23I2
24A2
24A3
24A4
24A5
25D1
31I8
25D2
30D7
25D6
30F1
25D7
30F3
25D8
30F9
25E1
30F6
25E2
30G2
25E3
30G4
Species
25E4
25E6
25E8
25E9
25D3
25D4
25E5
25E7
25F1
26I3
26I4
23F9
23G1
23G3
23G6
23G9
23H3
23H6
23H7
25A1
25A5
25A6
25A7
25A8
25B1
25B3
25B4
25B5
25B6
25B7
25B9
23F8
23G2
23H5
25B2
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
30G6
30H3
30H6
30H7
30E2
30E7
30G8
30H5
30H9
32A7
32B1
31C3
31D6
31D9
31E2
31E3
31E7
31F2
31F4
31F5
31F7
31F9
31G3
31E9
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Amphilophus citrinellus
Sampling
Location
Date
9/5/09
9/5/09
9/5/09
9/5/09
9/5/09
9/5/09
9/5/09
9/5/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
9/9/09
Isletas
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/14/09
9/14/09
9/5/09
9/5/09
9/5/09
9/5/09
9/5/09
9/5/09
9/5/09
9/5/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/5/09
9/5/09
9/5/09
9/9/09
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Managua Miraflores
Managua Miraflores
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
DNA/RNA sequencing/GenBank accession numbers
mtControl
ednrb1
phpt1
RNA sequencing BNIP3
JX402280
JX402217
JX402281
JX402218
JX402282
JX402219
JX402220
JX402283
JX402221
JX402284
JX402222
JX402285
JX402223
JX402286
JX402224
JX402288
JX402225
JX402289
JX402226
JX402227
y
JX402298
JX402228
JX402299
JX402229
JX402230
JX402292
JX402231
JX402287
JX402232
y
JX402293
JX402296
JX402297
JX402290
JX402367
JX402361
JX402365
JX402368
JX402375
JX402371
JX402364
JX402369
JX402378
JX402376
JX402363
JX402366
JX402351
JX402372
JX402359
JX402377
JX402349
JX402353
JX402374
JX402350
JX402358
JX402301
JX402302
JX402305
JX402306
JX402308
JX402310
JX402311
JX402312
JX402313
JX402314
JX402316
JX402309
JX402317
JX402318
JX402320
JX402300
JX402303
JX402307
JX402315
qPCR
Cldn7
Copb
His3
ACSL4
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
JX402233
JX402234
JX402235
JX402236
JX402294
JX402295
JX402298
JX402360
JX402354
Actb
JX402237
JX402238
JX402239
JX402240
JX402241
JX402242
JX402243
JX402244
JX402245
JX402246
JX402247
JX402248
JX402249
JX402250
JX402251
JX402252
JX402253
JX402254
JX402255
JX402256
25B8
23G5
23G7
23G8
23H1
25A3
25A4
25A9
25C1
25C6
28A3
28C6
35A1
35A2
35A3
35A4
35A5
35A6
35A7
35A8
35B6
31G2
31C9
31D4
31E5
31G6
31H7
32G6
32H7
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Amphilophus labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
Lobochilotes labiatus
36B3
36B4
36H7
43D7
81A2
43D8
81A5
43E4
81B9
43E5
81B4
43E6
44G8
44G9
44H1
44H3
44H5
44H6
36H8
43D9
81A7
43E1
81B1
43E2
81B3
43E3
81B7
44H4
43D6
81A3
55D1
81H9
55D2
81I2
55D8
79A5
55D9
79A9
BIB4
BMB4
BIC4
BMC4
BIC6
BMC6
BIC7
BMC7
BIC9
BMC9
additional Tropheini species for phylogenetic analyses:
Species
Astatotilapia burtoni
Ctenochromis horei
9/9/09
9/5/09
9/5/09
9/5/09
9/5/09
9/9/09
9/9/09
9/9/09
9/9/09
9/9/09
9/18/09
9/20/09
2/21/10
2/21/10
2/21/10
2/21/10
2/21/10
2/21/10
2/21/10
2/21/10
2/21/10
2/22/10
2/22/10
2/23/10
2/28/10
2/28/10
2/28/10
2/28/10
2/28/10
3/1/10
3/1/10
3/1/10
3/1/10
3/1/10
3/1/10
2/23/10
2/28/10
2/28/10
2/28/10
2/28/10
3/1/10
2/28/10
3/11/10
3/11/10
3/11/10
3/11/10
7/20/11
7/20/11
7/20/11
7/20/11
7/20/11
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Isletas
Managua Miraflores
Ometepe, San Ramon
Mbita Island W
Mbita Island W
Mbita Island W
Mbita Island W
Mbita Island W
Mbita Island W
Mbita Island W
Mbita Island W
Mbita Island W
Mpulungu area
Mpulungu area
Kasakalawe Lodge
Toby's Place
Toby's Place
Toby's Place
Toby's Place
Toby's Place
Toby's Place
Toby's Place
Toby's Place
Toby's Place
Toby's Place
Toby's Place
Kasakalawe Lodge
Toby's Place
Toby's Place
Toby's Place
Toby's Place
Toby's Place
Toby's Place
Mpulungu area
Mpulungu area
Mukaka
Mukaka
Toby`s place
Toby`s place
Toby`s place
Toby`s place
Toby`s place
JX402370
JX402373
JX402355
JX402356
JX402357
JX402352
JX402348
JX402362
J
JX402388
JX402383
JX402398
JX402399
JX402400
JX402405
JX402391
JX402392
JX402401
JX402404
JX402406
JX402403
JX402379
JX402407
JX402390
JX402381
JX402382
JX402395
JX402386
JX402380
JX402396
JX402387
JX402402
JX402389
JX402384
JX402385
JX402393
JX402394
JX402397
JX402319
JX402304
JX402321
JX402322
JX402323
JX402324
JX402325
JX402326
JX402327
JX402328
JX402329
JX402330
JX402331
JX402333
JX402334
JX402335
JX402340
JX402341
JX402342
JX402343
JX402344
JX402345
JX402346
JX402347
JX402332
JX402336
JX402337
JX402338
JX402339
JX402257
JX402278
JX402263
JX402266
JX402268
JX402262
JX402279
JX402259
JX402258
JX402267
JX402275
JX402277
JX402261
JX402260
JX402264
JX402273
JX402265
JX402270
JX402271
JX402269
JX402276
JX402272
JX402274
y
y
y
y
y
mtControl
AY930000
AY301952
ednrb1
JF900252
JF900262
phpt1
JF900181
JF900191
ND2
JF900319
EU753935
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
y
Gnathochromis pfefferi
Interochromis loockii
Limnotilapia dardennii
Lobochilotes labiatus
Petrochromis ephippium
Petrochromis famula
Petrochromis fasciolatus
Petrochromis macrognathus
Petrochromis polyodon
Pseudosimochromis curvifrons
Simochromis babaulti
Simochromis diagramma
Tropheus moorii
additional Amphilophus citrniellus mitochondrial control region sequences:
ampcit1
ampcit2
ampcit3
ampcit4
ampcit5
ampcit6
ampcit7
ampcit8
ampcit9
ampcit10
ampcit11
ampcit12
ampcit13
ampcit14
ampcit15
ampcit16
ampcit17
ampcit18
ampcit19
ampcit20
ampcit21
ampcit22
ampcit23
ampcit24
ampcit25
ampcit26
ampcit27
ampcit28
ampcit29
ampcit30
ampcit31
AY301954
GQ995855
AY301956
AY301958
AY301959
AY301960
GQ995911
AY929963
AY301967
AY301973
AY301975
AY301977
AY930020
AY567011
AY567018
AY567012
AY567013
AY567014
AY567015
AY567016
AY567017
EF219270
EF219269
EF219268
EF219252
EF219251
EF219250
EF219249
EF219248
EF219247
AY567470
AY567469
AY567468
AY567467
AY567466
AY567465
AY567464
AY567463
AY567462
AY567461
AY567460
AY567459
AY567458
AY567457
JF900269
JF900304
JF900285
JF900286
JF900300
JF900301
JF900325
JF900304
JF900305
JF900307
JF900309
JF900310
JF900314
JF900198
JF900232
JF900214
JF900215
JF900229
JF900230
JF900231
JF900233
JF900234
JF900236
JF900238
JF900239
JF900243
U07248
JF900322
GQ995724
U07254
JF900323
JF900324
JF900325
AY930068
JF900326
GQ995777
GQ995782
AY930087
AY930093