PCR survey of the Lightfish Gonostoma bathyphilum

Raw Data

  • PCR fragments of posterior Hox genes
  • translated sequences
  • Neighbor joining analysis of translated sequences

    • Determination of Paralog Group Identities

    Trees 3 4
    PG Sequence NJ pars A B C D A B C D Comments
    9 NJ   MP  
    Gb161-64-T C9 (0.45) C9 (0.27) * 0.2032 0.5340 0.2628 [0|1] [0|1] 0.5415 [3|3] [0|1]
    Gb166-65 D9 (0.58) D9 (0.40) 0.2351 * 0.3209 0.4440 [0|0] [0|1] 0.3850 [1|1] 0.4561 [3|2]
    Gb160-1-38 B9 (0.44) B9 (0.20) 0.2999 0.5171 0.1830 * [0|1] 0.5200 [3|3] [0|1] [0|1] ( Hi 9-3 )
    Gb160-1-19 A9a (0.76) A9a (0.51) 0.4758 0.3070 0.2172 * 0.5046 [3|3] [0|1] [0|1] [0|1]
    Gb161-61 A9b (0.77) A9b (0.62) 0.4358 0.2459 0.3182 * 0.4418 [3|3] [0|1] [0|1] [0|1]
    10 NJ   MP  
    Gb166-54 A10b (0.28) 0.4514 * 0.3192 0.2294 0.4311 [3|2] [0|1] 0.3684 [1|1] [0|0]
    Gb166B-4 A10 (0.22) A10 (0.17) 0.4620 * 0.2863 0.2518 0.4474 [3|3] [0|1] [0|1] [0|1] (Hi10-1,Hi10-2)
    Gb161-51-T C10 (0.25) C10 (0.12) * 0.2582 0.4779 0.2636 [0|1] [0|1] 0.5152 [3|3] [0|1] (Hi 10-4)
    Gb166-12 B10 (0.32) B10 (0.36) 0.3243 0.3454 * 0.3303 0.3895 [2|1] 0.3708 [3|1] [0|0] [0|0]
    Gb161-57- =Gb166-12
    11 NJ   MP  
    Gb166-55 A11/C11 A11/C11 0.269 * 0.4989 0.2312
    Gb166-81 A11 (0.19) A11 (0.18) 0.4831 * 0.1796 0.3373 (Hi11-1,Hi11-2)
    12 NJ   MP   C-und C-dupl D
    Gb160-1-33 D12 (0.64) D12 (0.53) 0.1886 0.2047 0.6967
    13 NJ   MP  
    Gb166-34 A13a (0.41) A13a (0.31) 0.4361 * 0.2475 0.3163 0.5638 [3|3] [0|1] [0|1] [0|1] (Hi13-1)
    Gb160-1-5 C13 (0.48) C13 (0.40) * 0.2163 0.5543 0.2294 [0|0] 0.3868 [1|1] 0.6072 [2|2] [0|1]
    Gb166B-5 C13 (0.48) C13 (0.40) * 0.2212 0.5408 0.2380 [0|1] [0|1] 0.5891 [3|1] [0|1]
    Gb160-1-22 B13 (0.38) HfD13 (0.27) 0.2467 0.4390 * 0.3143 0.3340 [1|1] 0.4032 [2|1] 0.3629 [1|1] [0|1]
    Gb160-1-23 D13 (0.22) D13 (0.09) 0.3218 0.3267 * 0.3515 0.3882 [2|1] [0|1] 0.3886 [1|1] 0.3794 [1|1]
    Gb372A-a13 A13b (0.24) A13b (0.11) 0.4319 * 0.3005 0.2676 0.5178 [3|3] [0|1] [0|1] [0|1]

    Determination of Teleost paralog group

    PG Sequence PG' Undup a b NJ
    9 [NJ] Gb161-64-T C9 C9a (0.20)
    Gb166-65 D9 0.4681 0.3803 0.1516 D9a (0.58)
    Gb160-1-38 B9 B9a (0.67)
    Gb160-1-19 A9 0.1711 0.5927 0.2361 A9a (0.49)
    Gb161-61 A9 0.3068 0.1722 0.5210 A9b (0.76)
    10 [NJ] Gb166-54 A10 0.2431 0.3170 0.4399 A10b (0.26)
    Gb166B-4 A10 0.3336 0.1629 0.5036 ? (*)
    Gb161-51-T C10 C10a (0.42)
    Gb166-12 B10 B10a (0.39)
    11 [NJ] Gb166-55 C11 (0.4711) (0.1692) (0.3564) ? (*)
    Gb166-81 A11 0.2586 0.3305 0.4110 A11b (0.16)
    12 [NJ] Gb160-1-33 D12 D12a (0.66)
    13 [NJ] Gb166-34 A13 0.2841 0.4989 0.2170 A13a (0.62)
    Gb160-1-5 C13 0.4010 0.3162 0.2828
    Gb166B-5 C13 0.4640 0.2656 0.2704 ? (*)
    Gb160-1-22 B13 ? (*)
    Gb160-1-23 D13 ? (*)
    Gb372A-a13 A13 0.4001 0.2664 0.3335 A13b (0.25)