Phylogentic Comparison of SA/CA Cichlids (emphasis on CA)

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B

bgolfer88

Feeder Fish
MFK Member
Nov 28, 2009
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VA
Thought this might be interesting. Based of protein sequence of Cytochrome B (gene cytb). If anyone has any other cichlid they would like to see I can add and update. Originally created based on my interest in hybrids. Obviously SA can't hybridize with CA but thought I'd compare them anyway to see (I've come across 1, maybe 2 instances of seemingly ligit GT hybrids). Enjoy!

Cichlid tree.png

Sequence type explicitly set to Protein
Sequence format is Pearson
Sequence 1: Convict 378 aa
Sequence 2: Firemouth 373 aa
Sequence 3: RedDevil 369 aa
Sequence 4: Midas 369 aa
Sequence 5: JackDempsey 378 aa
Sequence 6: Texas 378 aa
Sequence 7: Mayan 378 aa
Sequence 8: RedTerror 354 aa
Sequence 9: Jaguar 374 aa
Sequence 10: Cuban 378 aa
Sequence 11: Trimac 378 aa
Sequence 12: RedHead 359 aa
Sequence 13: Blackbelt 359 aa
Sequence 14: TwoBand 359 aa
Sequence 15: TailBar 359 aa
Sequence 16: GreenTerror 370 aa
Sequence 17: BlueAcara 376 aa
Sequence 18: Dovii 374 aa
Sequence 19: BlackAcara 370 aa
Sequence 20: Salvini 378 aa
Sequence 21: TBarSajica_ 378 aa
Sequence 22: Severum 377 aa
Sequence 23: Festivum 378 aa
Sequence 24: BlueDiscus 378 aa
Sequence 25: Angel 378 aa
Start of Pairwise alignments
Aligning...

Sequences (1:2) Aligned. Score: 95
Sequences (1:3) Aligned. Score: 94
Sequences (1:4) Aligned. Score: 95
Sequences (1:5) Aligned. Score: 95
Sequences (1:6) Aligned. Score: 96
Sequences (1:7) Aligned. Score: 97
Sequences (1:8) Aligned. Score: 94
Sequences (1:9) Aligned. Score: 97
Sequences (1:10) Aligned. Score: 96
Sequences (1:11) Aligned. Score: 97
Sequences (1:12) Aligned. Score: 96
Sequences (1:13) Aligned. Score: 96
Sequences (1:14) Aligned. Score: 97
Sequences (1:15) Aligned. Score: 97
Sequences (1:16) Aligned. Score: 94
Sequences (1:17) Aligned. Score: 93
Sequences (1:18) Aligned. Score: 94
Sequences (1:19) Aligned. Score: 94
Sequences (1:20) Aligned. Score: 96
Sequences (1:21) Aligned. Score: 97
Sequences (1:22) Aligned. Score: 95
Sequences (1:23) Aligned. Score: 95
Sequences (1:24) Aligned. Score: 94
Sequences (1:25) Aligned. Score: 93
Sequences (2:3) Aligned. Score: 95
Sequences (2:4) Aligned. Score: 95
Sequences (2:5) Aligned. Score: 96
Sequences (2:6) Aligned. Score: 97
Sequences (2:7) Aligned. Score: 97
Sequences (2:8) Aligned. Score: 94
Sequences (2:9) Aligned. Score: 97
Sequences (2:10) Aligned. Score: 97
Sequences (2:11) Aligned. Score: 97
Sequences (2:12) Aligned. Score: 97
Sequences (2:13) Aligned. Score: 97
Sequences (2:14) Aligned. Score: 97
Sequences (2:15) Aligned. Score: 97
Sequences (2:16) Aligned. Score: 94
Sequences (2:17) Aligned. Score: 93
Sequences (2:18) Aligned. Score: 94
Sequences (2:19) Aligned. Score: 94
Sequences (2:20) Aligned. Score: 97
Sequences (2:21) Aligned. Score: 97
Sequences (2:22) Aligned. Score: 95
Sequences (2:23) Aligned. Score: 96
Sequences (2:24) Aligned. Score: 94
Sequences (2:25) Aligned. Score: 94
Sequences (3:4) Aligned. Score: 96
Sequences (3:5) Aligned. Score: 95
Sequences (3:6) Aligned. Score: 95
Sequences (3:7) Aligned. Score: 95
Sequences (3:8) Aligned. Score: 91
Sequences (3:9) Aligned. Score: 96
Sequences (3:10) Aligned. Score: 95
Sequences (3:11) Aligned. Score: 97
Sequences (3:12) Aligned. Score: 95
Sequences (3:13) Aligned. Score: 95
Sequences (3:14) Aligned. Score: 95
Sequences (3:15) Aligned. Score: 94
Sequences (3:16) Aligned. Score: 91
Sequences (3:17) Aligned. Score: 90
Sequences (3:18) Aligned. Score: 94
Sequences (3:19) Aligned. Score: 92
Sequences (3:20) Aligned. Score: 94
Sequences (3:21) Aligned. Score: 96
Sequences (3:22) Aligned. Score: 93
Sequences (3:23) Aligned. Score: 95
Sequences (3:24) Aligned. Score: 92
Sequences (3:25) Aligned. Score: 92
Sequences (4:5) Aligned. Score: 96
Sequences (4:6) Aligned. Score: 95
Sequences (4:7) Aligned. Score: 96
Sequences (4:8) Aligned. Score: 92
Sequences (4:9) Aligned. Score: 97
Sequences (4:10) Aligned. Score: 96
Sequences (4:11) Aligned. Score: 97
Sequences (4:12) Aligned. Score: 96
Sequences (4:13) Aligned. Score: 96
Sequences (4:14) Aligned. Score: 96
Sequences (4:15) Aligned. Score: 95
Sequences (4:16) Aligned. Score: 91
Sequences (4:17) Aligned. Score: 91
Sequences (4:18) Aligned. Score: 94
Sequences (4:19) Aligned. Score: 93
Sequences (4:20) Aligned. Score: 95
Sequences (4:21) Aligned. Score: 97
Sequences (4:22) Aligned. Score: 94
Sequences (4:23) Aligned. Score: 95
Sequences (4:24) Aligned. Score: 93
Sequences (4:25) Aligned. Score: 93
Sequences (5:6) Aligned. Score: 97
Sequences (5:7) Aligned. Score: 97
Sequences (5:8) Aligned. Score: 96
Sequences (5:9) Aligned. Score: 97
Sequences (5:10) Aligned. Score: 97
Sequences (5:11) Aligned. Score: 97
Sequences (5:12) Aligned. Score: 97
Sequences (5:13) Aligned. Score: 97
Sequences (5:14) Aligned. Score: 97
Sequences (5:15) Aligned. Score: 96
Sequences (5:16) Aligned. Score: 93
Sequences (5:17) Aligned. Score: 93
Sequences (5:18) Aligned. Score: 95
Sequences (5:19) Aligned. Score: 94
Sequences (5:20) Aligned. Score: 96
Sequences (5:21) Aligned. Score: 97
Sequences (5:22) Aligned. Score: 96
Sequences (5:23) Aligned. Score: 97
Sequences (5:24) Aligned. Score: 94
Sequences (5:25) Aligned. Score: 94
Sequences (6:7) Aligned. Score: 97
Sequences (6:8) Aligned. Score: 95
Sequences (6:9) Aligned. Score: 97
Sequences (6:10) Aligned. Score: 97
Sequences (6:11) Aligned. Score: 97
Sequences (6:12) Aligned. Score: 98
Sequences (6:13) Aligned. Score: 98
Sequences (6:14) Aligned. Score: 98
Sequences (6:15) Aligned. Score: 98
Sequences (6:16) Aligned. Score: 94
Sequences (6:17) Aligned. Score: 93
Sequences (6:18) Aligned. Score: 95
Sequences (6:19) Aligned. Score: 95
Sequences (6:20) Aligned. Score: 98
Sequences (6:21) Aligned. Score: 97
Sequences (6:22) Aligned. Score: 96
Sequences (6:23) Aligned. Score: 96
Sequences (6:24) Aligned. Score: 95
Sequences (6:25) Aligned. Score: 95
Sequences (7:8) Aligned. Score: 95
Sequences (7:9) Aligned. Score: 98
Sequences (7:10) Aligned. Score: 97
Sequences (7:11) Aligned. Score: 98
Sequences (7:12) Aligned. Score: 98
Sequences (7:13) Aligned. Score: 98
Sequences (7:14) Aligned. Score: 97
Sequences (7:15) Aligned. Score: 97
Sequences (7:16) Aligned. Score: 93
Sequences (7:17) Aligned. Score: 93
Sequences (7:18) Aligned. Score: 95
Sequences (7:19) Aligned. Score: 95
Sequences (7:20) Aligned. Score: 96
Sequences (7:21) Aligned. Score: 97
Sequences (7:22) Aligned. Score: 96
Sequences (7:23) Aligned. Score: 97
Sequences (7:24) Aligned. Score: 95
Sequences (7:25) Aligned. Score: 94
Sequences (8:9) Aligned. Score: 95
Sequences (8:10) Aligned. Score: 95
Sequences (8:11) Aligned. Score: 95
Sequences (8:12) Aligned. Score: 92
Sequences (8:13) Aligned. Score: 92
Sequences (8:14) Aligned. Score: 92
Sequences (8:15) Aligned. Score: 92
Sequences (8:16) Aligned. Score: 91
Sequences (8:17) Aligned. Score: 90
Sequences (8:18) Aligned. Score: 92
Sequences (8:19) Aligned. Score: 92
Sequences (8:20) Aligned. Score: 94
Sequences (8:21) Aligned. Score: 94
Sequences (8:22) Aligned. Score: 93
Sequences (8:23) Aligned. Score: 95
Sequences (8:24) Aligned. Score: 92
Sequences (8:25) Aligned. Score: 93
Sequences (9:10) Aligned. Score: 98
Sequences (9:11) Aligned. Score: 99
Sequences (9:12) Aligned. Score: 98
Sequences (9:13) Aligned. Score: 98
Sequences (9:14) Aligned. Score: 98
Sequences (9:15) Aligned. Score: 97
Sequences (9:16) Aligned. Score: 94
Sequences (9:17) Aligned. Score: 92
Sequences (9:18) Aligned. Score: 96
Sequences (9:19) Aligned. Score: 94
Sequences (9:20) Aligned. Score: 97
Sequences (9:21) Aligned. Score: 99
Sequences (9:22) Aligned. Score: 96
Sequences (9:23) Aligned. Score: 97
Sequences (9:24) Aligned. Score: 95
Sequences (9:25) Aligned. Score: 95
Sequences (10:11) Aligned. Score: 98
Sequences (10:12) Aligned. Score: 97
Sequences (10:13) Aligned. Score: 97
Sequences (10:14) Aligned. Score: 97
Sequences (10:15) Aligned. Score: 96
Sequences (10:16) Aligned. Score: 94
Sequences (10:17) Aligned. Score: 92
Sequences (10:18) Aligned. Score: 95
Sequences (10:19) Aligned. Score: 94
Sequences (10:20) Aligned. Score: 96
Sequences (10:21) Aligned. Score: 97
Sequences (10:22) Aligned. Score: 96
Sequences (10:23) Aligned. Score: 96
Sequences (10:24) Aligned. Score: 95
Sequences (10:25) Aligned. Score: 94
Sequences (11:12) Aligned. Score: 98
Sequences (11:13) Aligned. Score: 98
Sequences (11:14) Aligned. Score: 97
Sequences (11:15) Aligned. Score: 97
Sequences (11:16) Aligned. Score: 94
Sequences (11:17) Aligned. Score: 92
Sequences (11:18) Aligned. Score: 96
Sequences (11:19) Aligned. Score: 94
Sequences (11:20) Aligned. Score: 96
Sequences (11:21) Aligned. Score: 98
Sequences (11:22) Aligned. Score: 96
Sequences (11:23) Aligned. Score: 97
Sequences (11:24) Aligned. Score: 94
Sequences (11:25) Aligned. Score: 94
Sequences (12:13) Aligned. Score: 100
Sequences (12:14) Aligned. Score: 99
Sequences (12:15) Aligned. Score: 98
Sequences (12:16) Aligned. Score: 94
Sequences (12:17) Aligned. Score: 93
Sequences (12:18) Aligned. Score: 96
Sequences (12:19) Aligned. Score: 96
Sequences (12:20) Aligned. Score: 98
Sequences (12:21) Aligned. Score: 97
Sequences (12:22) Aligned. Score: 96
Sequences (12:23) Aligned. Score: 97
Sequences (12:24) Aligned. Score: 94
Sequences (12:25) Aligned. Score: 94
Sequences (13:14) Aligned. Score: 99
Sequences (13:15) Aligned. Score: 98
Sequences (13:16) Aligned. Score: 94
Sequences (13:17) Aligned. Score: 93
Sequences (13:18) Aligned. Score: 96
Sequences (13:19) Aligned. Score: 96
Sequences (13:20) Aligned. Score: 98
Sequences (13:21) Aligned. Score: 97
Sequences (13:22) Aligned. Score: 96
Sequences (13:23) Aligned. Score: 97
Sequences (13:24) Aligned. Score: 94
Sequences (13:25) Aligned. Score: 94
Sequences (14:15) Aligned. Score: 99
Sequences (14:16) Aligned. Score: 93
Sequences (14:17) Aligned. Score: 93
Sequences (14:18) Aligned. Score: 95
Sequences (14:19) Aligned. Score: 95
Sequences (14:20) Aligned. Score: 98
Sequences (14:21) Aligned. Score: 98
Sequences (14:22) Aligned. Score: 96
Sequences (14:23) Aligned. Score: 97
Sequences (14:24) Aligned. Score: 94
Sequences (14:25) Aligned. Score: 94
Sequences (15:16) Aligned. Score: 93
Sequences (15:17) Aligned. Score: 93
Sequences (15:18) Aligned. Score: 95
Sequences (15:19) Aligned. Score: 95
Sequences (15:20) Aligned. Score: 97
Sequences (15:21) Aligned. Score: 97
Sequences (15:22) Aligned. Score: 96
Sequences (15:23) Aligned. Score: 96
Sequences (15:24) Aligned. Score: 94
Sequences (15:25) Aligned. Score: 94
Sequences (16:17) Aligned. Score: 95
Sequences (16:18) Aligned. Score: 91
Sequences (16:19) Aligned. Score: 93
Sequences (16:20) Aligned. Score: 93
Sequences (16:21) Aligned. Score: 93
Sequences (16:22) Aligned. Score: 92
Sequences (16:23) Aligned. Score: 94
Sequences (16:24) Aligned. Score: 92
Sequences (16:25) Aligned. Score: 92
Sequences (17:18) Aligned. Score: 90
Sequences (17:19) Aligned. Score: 93
Sequences (17:20) Aligned. Score: 93
Sequences (17:21) Aligned. Score: 92
Sequences (17:22) Aligned. Score: 92
Sequences (17:23) Aligned. Score: 93
Sequences (17:24) Aligned. Score: 91
Sequences (17:25) Aligned. Score: 91
Sequences (18:19) Aligned. Score: 92
Sequences (18:20) Aligned. Score: 95
Sequences (18:21) Aligned. Score: 96
Sequences (18:22) Aligned. Score: 94
Sequences (18:23) Aligned. Score: 95
Sequences (18:24) Aligned. Score: 92
Sequences (18:25) Aligned. Score: 92
Sequences (19:20) Aligned. Score: 95
Sequences (19:21) Aligned. Score: 94
Sequences (19:22) Aligned. Score: 94
Sequences (19:23) Aligned. Score: 94
Sequences (19:24) Aligned. Score: 93
Sequences (19:25) Aligned. Score: 93
Sequences (20:21) Aligned. Score: 96
Sequences (20:22) Aligned. Score: 95
Sequences (20:23) Aligned. Score: 96
Sequences (20:24) Aligned. Score: 93
Sequences (20:25) Aligned. Score: 94
Sequences (21:22) Aligned. Score: 96
Sequences (21:23) Aligned. Score: 97
Sequences (21:24) Aligned. Score: 95
Sequences (21:25) Aligned. Score: 94
Sequences (22:23) Aligned. Score: 96
Sequences (22:24) Aligned. Score: 95
Sequences (22:25) Aligned. Score: 94
Sequences (23:24) Aligned. Score: 95
Sequences (23:25) Aligned. Score: 94
Sequences (24:25) Aligned. Score: 94

Cichlid tree.png
 
Interesting. What was your source for the Cytochrome B from individuals? Generic store bought individuals (that could have mixed lineage?) or wild fish? How do you feel about the use of mitochondrial DNA for genetic analysis vs. nuclear DNA?

It obviously got some relationships correct, but also got some pretty incorrect.
 
I agree very interesting. I would also like to hear more about the specifics.
 
I used the Uniprot website/database, I think they draw from multiple sources so it is a good question if these are store or wild fish. My instincts say that the cytb data is probably accurate but yes, has limitations in comparison. I would love to take the time in the future to try to bang out a nDNA analysis. =) Or if anyone knows where one already is I'd love to see it. I found one but it was mostly Africans with CA/SA lumped as an outgroup.
 
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944184/pdf/1471-2148-10-279.pdf

http://www.sciencedirect.com.ezprox...ate.edu/science/article/pii/S1055790308003825

1-s20-S1055790308003825-gr2.jpg


1-s20-S1055790308003825-gr6.jpg


1-s20-S1055790308003825-gr1.jpg
 
Can you find that for SAs?
 
Azedenkae said:
Interesting. Have you thought about looking at the mitochondrial DNA? Last I checked ncbi has complete genomes for cichlids, might be worth a look at. Looking at the multiple genes would definitely create a more 'true' tree I reckon.
Click to expand...

Cytocrome B is mitochondrial DNA, which is usually less accurate than nuclear DNA for determining phylogeny.
 
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