Table 3 Codons putatively under positive selection in HIFA genes in Actinopterygii.

From: Genomic analysis of hypoxia inducible factor alpha in ray-finned fishes reveals missing Ohnologs and evidence of widespread positive selection

Gene

Episodic Selection

Pervasive Selection

HIF1A

51a, 57a, 60a, 62a, 65, 140, 271a, 354, 365a, 484, 525, 579, 590, 595, 609a, 695, 761a, 774a, 835, 841, 872, 875, 876a, 877, 931

835b

HIF2A

172, 204a, 210, 213, 219a, 222a, 224, 293, 304a, 306a, 357a, 371a, 373a, 380a, 382a, 385a, 386a, 388a, 389a, 392a, 394a, 396, 397a, 407, 425a, 452a, 577, 635a, 674a, 676, 694a, 746, 787a, 873, 921, 999a, 1063, 1087, 1090, 1093a, 1095

94, 1063b,c

HIF3A

26, 188a, 210a, 265a, 268a, 339, 436, 457, 460, 464, 478a, 479a, 494, 529a, 590, 600a, 605a, 645, 661a, 675a, 713a, 772a, 773a, 774, 775a, 788a, 792a, 802a, 807, 829a, 830a, 831a, 836a, 842a

457, 774

HIF4A

68, 115, 124, 147, 287, 300, 362, 382, 511, 530, 633, 666, 683, 703, 735, 774, 783a, 796a

71, 382, 654, 673, 703, 727

  1. Episodic positive selection was detected by MEME and pervasive positive selection was detected by FEL. Codons detected by both tests are shown in bold type. Codon number corresponds to the position in the multiple sequence alignment of all HIFA genes used in each analysis. See Supplemental Table S3 for amino acid identities in each species for each HIFA paralog.
  2. aEpisodic positive selection supported by BUSTED evidence ratio > 2.
  3. bPervasive positive selection supported by SLAC posterior probability > 0.95.
  4. cPervasive positive selection supported by FUBAR posterior probability > 0.95.