Table 1.
Duplicated Fish Genes and Human Orthologs
| Human Query Sequences | Each Column Lists Members of a Clade That is Orthologous to the Human Query Sequence | NJ | QP | AS | |
| ATP1B1(4502277) | Danio9789577 | Danio11096273, Anguilla 1703468, Anguilla 7406523,TakifuguJGI22524 | + | − | + |
| ATP1B2(4502279) | Danio 9789579 | Danio 14150727,Takifugu JGI789 | + | + | + |
| ATP1B3(4502278) | Danio 974774, Anguilla7406521 | Danio 9837579, TakifuguJGI9802 | + | + | + |
| BMP2 (4557369) | Danio2149148 | Danio 2804175, TakifuguJGI7838 | + | + | + |
| CYP19 (13904858) | Danio12655890, Carassius 3913347, Oreochromis4838530, Oreochromis 4838536, TakifuguJGI6225, Pimephales 14041612 | Danio 12655892,Carassius 2662332, Oreochromis 3913346,Oreochromis 4838538, Takifugu JGI22275,Ictalurus 3913357, Oncoryhnchus 228574,Oryzias 3913355, Dicentrarchus 14589321,Hippoglossus 13620178, Paralicthys4239990 | + | + | + |
| DLL(10518497) | Danio 2809389, TakifuguJGI3940 | Danio 1888392, TakifuguJGI18204 | + | + | − |
| DLX2 (4758168) | Danio2842748 | Danio 108243, TakifuguJGI119697 | + | + | + |
| DLX4 (4503343) | Danio2842751 | Danio 2842750 | + | + | + |
| EFNA5(4503487) | Danio 2494365, TakifuguJGI4301 | Danio 2462953, TakifuguJGI34618 | − | − | − |
| EN1 (7710119) | Danio4322044, Takifugu JGI28510 | Danio 417127,Takifugu JGI32850 | − | − | − |
| EN2(11422302) | Danio 417128 | Danio 417129,Takifugu JGI7515 | − | − | − |
| EPHB4(4758290) | Danio 3163942, TakifuguJGI26074 | Danio 3005901, TakifuguJGI17145 | + | + | + |
| FKH1 (4503735) | Danio12004940 | Danio 12004938, TakifuguJGI9390 | − | − | − |
| FKH5 (8134472) | Danio2982347, Takifugu JGI20315 | Danio 2982343,Takifugu JGI3282 | − | − | + |
| FLOT1(5031699) | Danio 12751185, Carassius 2190561,Takifugu JGI8518 | Danio 12751187,Carassius 12751189, TakifuguJGI3374 | − | + | + |
| FZD8 (1033460) | Danio4164471, Takifugu JGI14550 | Danio 4335927,Takifugu JGI21332 | − | + | + |
| Gdf6(1707885 Bos) | Danio 914116, TakifuguJGI7189 | Danio 1906321, TakifuguJGI32443 | − | + | + |
| HOXB6 (32369) | Danio62530, Takifugu JGI5208 | Danio4322075 | − | − | + |
| HOXC6 (4758554) | Danio4322098, Takifugu 2341089 | Danio4322100 | − | − | + |
| HSP71 (5729877) | Danio1865782, Danio 2495341 | Danio 2245606,Oncorhychus 232285, Ictalurus 1346318,Paralichthys 3513540, Oryzias4589737 | + | − | − |
| HSPA1(5123454) | Takifugu JGI656, Xiphophorus17061835, Paralichthys 11277120 | Takifugu1620388, Xiphophorus 17061837, Oncorhychus17129570, Oncorhychus 2495346, Danio7061841, Danio 7861932, Oreochromis3004463, Oryzias 9652348 | + | + | + |
| HUR(4503551) | Danio 6694223, TakifuguJGI20049 | Danio 6694225, TakifuguJGI16540 | − | + | + |
| ISL2 (14755347) | Danio1708564, Oncorhychus 1708565, TakifuguJGI18627 | Danio 1708561, Oncorhychus 1708557,Oncorhychus 1708558 | − | − | − |
| JAK2(4826776) | Danio 3687398, TakifuguJGI20041 | Danio 3687400, Takifugu JGI19673,Tetraodon 5918520 | − | − | − |
| KAL1(4557683) | Danio 6708056, TakifuguJGI14813 | Danio 6708054, TakifuguJGI16508 | + | + | + |
| L1CAM (4557707) | Danio1065716, Takifugu 7522081 | Danio 1065714,Takifugu JGI14258, Carassius11277081 | + | − | − |
| NGCAM(6651380) | Takifugu JGI1459 | Takifugu2856 | + | + | + |
| NRCAM(5729767) | Takifugu JGI2517 | Takifugu7031 | + | + | + |
| LDHB(12803117) | Takifugu JGI2932, Fundulus462491, Anguilla 4321147, Danio6048361 | Takifugu JGI30368, Fundulus555487 | + | + | + |
| LHX1 (13652710) | Danio2155289 | Danio 2497670 | + | − | − |
| MITF(4557755) | Danio 15341251, TakifuguJGI2179 | Danio 5726232, TakifuguJGI24563 | − | − | − |
| Msx3 (6754756Mus) | Danio 608511 | Danio 62543,Takifugu JGI6688, Tetraodon8187099 | + | + | + |
| MSX2 (4505269) | Danio62545, Takifugu JGI20308 | Danio608509 | − | + | − |
| Nodal2 (897598Xenopus) | Takifugu JGI17187,Danio 3540235 | TakifuguJGI2967 | + | + | + |
| NOG (4885523) | Danio4185744 | Danio 5410599, Takifugu3860047 | + | + | + |
| NOTCH (11275980) | Danio433867, Takifugu JGI3276 | Danio 2569968,Takifugu JGI22935 | − | + | + |
| NTN1(4758840) | Danio 2327065, TakifuguJGI27841 | Danio 2394302 | − | − | + |
| OPRD(4505509) | Danio 9837282, TakifuguJGI343 | Danio 7441620, TakifuguJGI9982 | + | − | − |
| OTX1 (417425) | Danio3024327, Takifugu JGI36992 | Danio3024322 | + | + | + |
| PAX2 (4557820) | Danio3420030, Oryzias 2344868 | Danio62550 | + | + | + |
| PAX6 (4505615) | Danio62549, Astyanax 2369651 | Danio 3779238,Takifugu 3402199, Oryzias4426551 | + | + | + |
| POU3F3 (5453936) | Danio1730449, Takifugu JGI15850 | Danio 1730450,Takifugu JGI3511 | − | − | − |
| RARA(4160009) | Danio 704370, Takifugu 4972006,Salmo 9931536 | Danio 215026, TakifuguJGI11888 | + | + | + |
| Rx (6002393Gallus) | Danio 2240028, Takifugu JGI10186,Oryzias 7635917 | Danio 9903605, TakifuguJGI19484 | − | + | + |
| RXRB (1350911) | Danio1046297, Takifugu JGI191 | Danio 1046299,Takifugu JGI4030, Scophthalmus14994052 | + | − | + |
| SHH(4506939) | Danio6136068 | Danio6174983, Takifugu JGI13503, Paralichthys5441265 | + | + | + |
| SPON2(6912682) | Danio 2529223, TakifuguJGI14751 | Danio 2529221, TakifuguJGI7893 | − | − | − |
| SNAIL (5729673) | Danio545349, Takifugu 5830231 | Danio 841423,Takifugu 5830233 | + | + | + |
| SNAP25(134583) | Danio 3703098, Carassius548943 | Danio 3703100, Carassius548945 | − | − | − |
| SOX11 (4507160) | Danio4099262, Takifugu JGI7177 | Danio 7572946,Oncorhychus 2826913 | + | + | + |
| SPON1(11320819) | Danio 2529224, TakifuguJGI8633 | Danio 2529226 | − | + | + |
| TCF3(11230858) | Danio 5281354 | Danio3769679 | + | + | + |
| TPI (4507644) | Danio15149249, Xiphophorus 15149253 | Danio 15149247,Xiphophorus 15149251 | − | − | + |
-
Paralogous fish genes and their human “pro-ortholog” shown on the same row. Orthologous fish genes listed in the same box. NCIBgi and JGI (for pufferfish) numbers shown. NJ = neighbor-joining. QP = quartet puzzling. AS = ASATURA (Van de Peer et al. 2002) analyses. The plus (+) symbol indicates that the topology reflected by the arrangement of genes in the table is the one in the NJ, QP, or ASATURA trees. The minus (−) symbol indicates that this phylogenetic analysis was carried out but that the resulting tree topology was not consistent with the arrangement of the genes in the table.
