Additional file 3
List of samples used for mtDNA and AFLP analyses with sample identifiers, mtDNA sequence accession numbers (superscript numbers indicate origin of sequences: 1: this study, 2: ref. 28, 3: ref. 29, 4: ref. 27, 5: ref. 50, 6: ref. 23), coordinates of sampling sites (if known) and assignment of samples to species (as suggested by Konings [25]) and colour lineages (defined by Schupke [24]). When more than one morph / species was sampled from a location, the species / morphs are given in parentheses with the locality. For each sample, asterisks in the last two columns indicate the use of AFLP and/or mtDNA sequence data in the analyses.
Sample 4376 4377 Tr10 Tr23 146 4367 4368 957 958 955 956 4529 4530 4531 959 1049 1050 Tr12 Tr13 4517 4518 4519 4140 4141 Accession # EF694249 EF6942501 AY6608264 AY6608274 Z120902 EF6942431 EF6942441 AJ4896453 AJ4896463 AJ4896433 AJ4896443 EF6942801 EF6942811 EF6942821 AJ4897053 AJ4920743 AJ4920773 AY6607754 AY6607764 EF6942311 EF6942321 EF6942331 EF6942351 EF6942361
1
Locality Bemba Bemba Bulombora Bulombora Bulu Point Chaitika Chaitika Chimba Chimba Chipimbi Chipimbi Chisanze Chisanze Chisanze Chisiki Funda Funda Halembe (T. brichardi) Halembe (T. brichardi) Halembe (T. duboisi) Halembe (T. duboisi) Halembe (T. duboisi) Ikola Ikola
Latidude Longitude (S) (E) Species (after Konings 1998) 03°37' 03°37' 05°02' 05°02' 06°01' 08°34' 08°34' 08°19' 08°19' 08°17' 08°17' 29°09' 29°09' 29°46' 29°46' 29°45' 30°47' 30°47' 30°32' 30°32' 30°34' 30°34' Tropheus sp. "black" Tropheus sp. "black" Tropheus brichardi Tropheus brichardi Tropheus sp. "black" Tropheus moorii Tropheus moorii Tropheus sp. "red" Tropheus sp. "red" Tropheus sp. "red" Tropheus sp. "red" Tropheus sp. "red" Tropheus sp. "red" Tropheus sp. "red" Tropheus sp. "red" Tropheus moorii Tropheus moorii Tropheus brichardi Tropheus brichardi Tropheus duboisi Tropheus duboisi Tropheus duboisi Tropheus sp. "Ikola" Tropheus sp. "Ikola"
Colour lineage (after Schupke 2003) 2 Blackbrown 2 Blackbrown 3 Yellow Fins 3 Yellow Fins 12 Kirschfleck 8 Rainbow 8 Rainbow 7 Striped forehead, red 7 Striped forehead, red 7 Striped forehead, red 7 Striped forehead, red 7 Striped forehead, red 7 Striped forehead, red 7 Striped forehead, red 7 Striped forehead, red 8 Rainbow 8 Rainbow 3 Yellow Fins 3 Yellow Fins 10 Tropheus duboisi 10 Tropheus duboisi 10 Tropheus duboisi 11 Kaiser 11 Kaiser
AFLP mtDNA
08°20' 08°46' 08°46' 05°44' 05°44' 05°44' 05°44' 05°44' 06°41' 06°41'
30°31' 30°59' 30°59' 29°55' 29°55' 29°55' 29°55' 29°55' 30°22' 30°22'
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5342 5344 5447 5448 4379 4380 722 723 724 4523 4524 4525 105 4370 4371 78 83 93 125 84 Tr16 Tr17 Tr8 Tr9 115 4511 4512 4513 Tr4 Tr5 686 961 704 705
EF6942371 EF6942381 EF6942391 EF6942401 EF6942511 EF6942521 AJ4897073 AJ4897083 AJ4896333 EF6942771 EF6942781 EF6942791 Z120772 EF6942451 EF6942461 Z120762 Z120752 Z120742 DQ2028335 Z120732 AY6607794 AY6607804 AY6607724 AY6607734 Z120552 EF6942681 EF6942691 EF6942701 AY6607684 AY6607694 AJ4920123 AJ4896863 AJ4920383 AJ4920763
Ikola North ("Kaiser") Ikola North ("Kaiser") Ikola North (T. polli) Ikola North (T .polli) Ilangi Ilangi Inangu Inangu Inangu Kabeyeye Kabeyeye Kabeyeye Kabimba Kachese Kachese Kala Kala Kala Kalambo Kalambo Kalya Kalya Kapampa Kapampa Kapampa Kapere Kapere Kapere Karilani Island Karilani Island Kasakalawe Kasanga Katoto Katoto
06°40' 06°40' 06°40' 06°40'
30°18' 30°18' 30°18' 30°18'
08°29' 08°29' 08°29'
30°41' 30°41' 30°41'
05°33' 08°29' 08°29' 08°08' 08°08' 08°08' 08°36' 08°36' 06°28' 06°28' 07°30' 07°30' 07°30'
29°20' 30°28' 30°28' 30°58' 30°58' 30°58' 31°11' 31°11' 30°00' 30°00' 30°12' 30°12' 30°12'
05°58' 05°58' 08°47' 08°26' 08°48' 08°48'
29°47' 29°47' 31°04' 31°08' 31°01' 31°01'
Tropheus sp. "Ikola" Tropheus sp. "Ikola" Tropheus annectens (syn. T. polli) Tropheus annectens (syn. T. polli) Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus brichardi Tropheus sp. "red" Tropheus sp. "red" Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus sp. "black" Tropheus sp. "black" Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii
11 Kaiser 11 Kaiser 4 Whimple 4 Whimple 7 Striped forehead, red 7 Striped forehead, red 7 Striped forehead, red 7 Striped forehead, red 7 Striped forehead, red 8 Rainbow 8 Rainbow 8 Rainbow 3 Yellow Fins 7 Striped forehead, red 7 Striped forehead, red 8 Rainbow 8 Rainbow 8 Rainbow 8 Rainbow 8 Rainbow 6 Striped forehead 6 Striped forehead 6 Striped forehead 6 Striped forehead 6 Striped forehead 8 Rainbow 8 Rainbow 8 Rainbow 12 Kirschfleck 12 Kirschfleck 8 Rainbow 8 Rainbow 8 Rainbow 8 Rainbow
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820 821 Tr30 2085 62 96 97 120 639 640 4417 4418 4499 4500 4501 Tr20 Tr21 4520 4521 4522 5475 5477 5478 5479 5480 5481 4300 4301 119 4382 4383 4374 4375 4514
AJ4920703 AJ2959133 AY6608364 AY6608304 Z120692 EF6942341 AY9299786 Z120872 AJ4896493 AJ4896503
EF6942571 EF6942581 EF6942591 AY6607834 AY6607844 EF6942741 EF6942751 EF6942761 EF6942831 EF6942841 EF6942851 EF6942861 EF6942871 EF6942881 EF6942411 EF6942421 AY6607634 EF6942531 EF6942541 EF6942471 EF6942481 EF6942711
Katukula Katukula Kavala Island Kavala Island Kiriza Kiriza Kiriza Kungwe Mountain Range Livua Livua Livua Livua Livua Livua Livua Lufubu Lufubu Mabilibili ("Kirschfleck") Mabilibili ("Kirschfleck") Mabilibili ("Kirschfleck") Mabilibili ("red belly") Mabilibili ("red belly") Mabilibili ("red belly") Mabilibili ("red belly") Mabilibili ("red belly") Mabilibili ("red belly") Mbita Island Mbita Island Mboko Moliro Moliro Mpimbwe Mpimbwe Murago
08°43' 08°43' 05°38' 05°38' 04°03' 04°03' 04°03' 06°01' 08°05' 08°05' 08°05' 08°05' 08°05' 08°05' 08°05' 08°32' 08°32'
30°57' 30°57' 29°24' 29°24' 29°13' 29°13' 29°13' 29°45' 30°32' 30°32' 30°32' 30°32' 30°32' 30°32' 30°32' 30°44' 30°44'
Tropheus moorii Tropheus moorii Tropheus annectens (syn. T. polli) Tropheus annectens (syn. T. polli) Tropheus sp. "black" Tropheus sp. "black" Tropheus sp. "black" Tropheus sp. "black" Tropheus sp. "red" Tropheus sp. "red" Tropheus sp. "red" Tropheus sp. "red" Tropheus sp. "red" Tropheus sp. "red" Tropheus sp. "red" Tropheus moorii Tropheus moorii Tropheus sp. "black" Tropheus sp. "black" Tropheus sp. "black" new morph new morph new morph new morph new morph new morph Tropheus moorii Tropheus moorii Tropheus sp. "black" Tropheus sp. "red" Tropheus sp. "red" Tropheus sp. "Mpimbwe" Tropheus sp. "Mpimbwe" Tropheus moorii
8 Rainbow 8 Rainbow 4 Whimple 4 Whimple 1 Black 1 Black 1 Black 12 Kirschfleck 7 Striped forehead, red 7 Striped forehead, red 7 Striped forehead, red 7 Striped forehead, red 7 Striped forehead, red 7 Striped forehead, red 7 Striped forehead, red 8 Rainbow 8 Rainbow 12 Kirschfleck 12 Kirschfleck 12 Kirschfleck new morph new morph new morph new morph new morph new morph 8 Rainbow 8 Rainbow 1 Black 7 Striped forehead, red 7 Striped forehead, red 9 Striped Blueeyes 9 Striped Blueeyes 8 Rainbow
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08°46' 08°46' 03°55' 08°12' 08°12' 07°08' 07°08' 07°03'
31°06' 31°06' 29°05' 30°34' 30°34' 30°30' 30°30' 29°47'
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4515 4516 4502 4503 4504 4385 4386 Tr1 Tr2 4508 4509 4510 4419 104 56 82 Tr25 643 644 4505 4507 128 129 Tr14 Tr15 4415 4416 831 832
EF6942721 EF6942731 EF6942601 EF6942611 EF6942621 EF6942551 EF6942561 AY6607654 AY6607664 EF6942651 EF6942661 EF6942671 EF6942891 Z120542 Z120502 Z120492 AY660786 AJ4921003 AJ4921013 EF6942631 EF6942641 Z757052 Z120482 AY6607774 AY6607784
AJ4896303 AJ4896313
Murago Murago Muzi Muzi Muzi Nakaku Nakaku Namansi Namansi Ndole Ndole Ndole Nvuna Island Nyanza Lac Rutunga Rutunga Siyeswe Tongwa Tongwa Ulwile Island Ulwile Island Wapembe North Wapembe North Wapembe South Wapembe South Zongwe Zongwe Zongwe Zongwe
07°03' 07°03'
29°47' 29°47'
08°40' 08°40' 07°32' 07°32'
30°54' 30°54' 30°36' 30°36'
07°26' 04°20' 03°40' 03°40' 06°21' 08°40' 08°40'
30°33' 29°35' 29°19' 29°19' 29°48' 30°53' 30°53'
07°54' 07°54' 08°00' 08°00' 07°18' 07°18' 07°18' 07°18'
30°49' 30°49' 30°53' 30°53' 30°08' 30°08' 30°08' 30°08'
Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus sp. "red" Tropheus sp. "red" Tropheus sp. "red" Tropheus brichardi Tropheus brichardi Tropheus sp. "black" Tropheus sp. "black" Tropheus sp. "black" Tropheus moorii Tropheus moorii Tropheus brichardi Tropheus brichardi Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii Tropheus moorii
8 Rainbow 8 Rainbow 8 Rainbow 8 Rainbow 8 Rainbow 8 Rainbow 8 Rainbow 8 Rainbow 8 Rainbow 7 Striped forehead, red 7 Striped forehead, red 7 Striped forehead, red 9 Striped Blueeyes 3 Yellow Fins 1 Black 1 Black 12 Kirschfleck 8 Rainbow 8 Rainbow 9 Striped Blueeyes 9 Striped Blueeyes 8 Rainbow 8 Rainbow 8 Rainbow 8 Rainbow 6 Striped forehead 6 Striped forehead 6 Striped forehead 6 Striped forehead
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