hAT-38_HM_1p 1 Kolobok-1_Bf2p hAT-20_HM_1p 1 Kolobok-2_Bf2p hAT-47_SM_1p 0.96 Kolobok-1_CTe_2p 1 hAT-24_LCh_1p Kolobok-2_Xt2p hAT-29_LCh_1p 0.852 Kolobok-1_Aqu_2p Cyprinodontiformes Kolobok-4_DR_2p Perciformes Anoplopomatidae 1 Lampriformes Kolobok-1_AP_1p Pomacentridae 0.992 Kolobok-1_AP_2p 0.963 Holocentriformes 0.9 Kolobok-1_SKow_2p 0.985 Cypriniformes Kolobok-1_NV2p Kolobok-12_CGi_2p Labriformes 0.848 Kolobok-2_CGi_2p Perciformes Notothenioidei Gobiiformes 0.737 Siluriformes Perciformes Serranidae Cypriniformes Spariformes 1 Perciformes Percidae 0.992 Perciformes Sebastidae Esociformes 0.874 Holocentriformes Centrachiformes Anguilliformes Salmoniformes Gadiformes 1 Cyprinodontiformes Polypteryformes 0.937 0.999 Perciformes Serranidae Cypriniformes 0.999 0.997 0.9 Gadiformes Scombriformes Holocentriformes Perciformes Anoplopomatidae * Esociformes Beryciformes 0.805 Cyprinodontiformes Aulopiformes 0.9 Gadiformes 0.924 Perciformes Liparidae Clupeiformes Anoplopomtidae (1/1) Anoplopoma fimbria Gadiformes Cypriniformes Mugilidae 0.82 Cyprinodontiformes Percidae (1/6) hAT (863 AA) (863 hAT Clupeiformes 0.999 Etheostoma spectabi Anoplopomtidae (1/1) Perciformes Percidae Gadiformes Kolobok (137 AA) (137 Kolobok Anoplopoma fimbria Serranidae (3/8) Pseudochromidae 0.923 Epinephelus coioides Trachichthyiformes Gadiformes Percidae (4/6) Scombriformes E. lanceolatus Centrachiformes Sander vitreus Gadiformes E. moara Sander lucioperca Spariformes 0.995 Cypriniformes Sebastidae (9/9) Perca flavescens Sebastes aleutianus Perca fluviatilis Moronidae S. koreanus Cypriniformes 0.958 Scombriformes Nothothenioidei (2/2) Trachichthyiformes S. minor Perciformes Anoplopomatidae * Cypriniformes S. nigrocinctus Notothenia coriiceps Gadiformes S. norvegicus Chionodraco myersi 0.996 Cyprinodontiformes Gadiformes S. nudus Perciformes Percidae S. ruvrivinctus Liparidae (2/2) Cypriniformes S. schlegelli Liparis tanakae S. steindachneri 0.2 Pseudoliparis sp. Supplemental Figure S2. Phylogenetic trees of amino acid sequences of transposases from longer elements related to the Y- (hAT) and X-specific (Kolobok) MITEs. Trees were rooted using Repbase sequences (in black) as an outgroup as they appear more distantly related. Different colors correspond to the different main orders in which related elements have been identified. Numbers above the main branch represent the robustness SH test. Perciformes sequences are in orange, and pink for Anoplopoma fimbria. The species names where sequences were found (among Perciformes) are indicated next to the trees, classified by families. Number of species out of number of sequenced species. The asterisk for Anoplopomatidae sequences indicates the sequence found in the new assembly (Other Anoplopoma fimbria sequences are from the NCBI assembly)..