Phylogeny of CmiERVs and other representative retroviruses. The phylogeny was reconstructed based on the retrovirus Pol protein sequences. Posterior probabilities are labeled near the selected nodes. The CmiERVs and the retroviruses of fish origin are highlighted in blue and orange, respectively. The numbers of the scaffolds where CmiERV fragments were identified are labeled near the corresponding tips. Abbreviation: ALV, Avian leukosis virus; BFV, Bovine foamy virus; BIV, Bovine immunodeficiency virus; BLV, Bovine leukemia virus; CAEV, Caprine arthritis-encephalitis virus; CoEFV, Coelacanth endogenous foamy virus; EFV, Equine foamy virus; EIAV, Equine infectious anemia virus; ERV-baboon, Baboon endogenous virus; FFV, Feline foamy virus; FIV, Feline immunodeficiency virus; FLV, Feline leukemia virus; GALV, Gibbon ape leukemia virus; GGERV, Gallus gallus endogenous retrovirus; GvaELV, Galeopterus variegatus endogenous lentivirus; HIV-1, Human immunodeficiency virus type 1; HIV-2, Human immunodeficiency virus type 2; HML1-9, Human MMTV-like 1–9; HTLV, Human T-cell leukemia virus; HERV, Human endogenous retrovirus; JDV, Jembrana disease virus; JSRV, Jaagsiekte sheep retrovirus; KoRV, Koala retrovirus; LDV, Lymphoproliferative disease virus; MDERV, Mus dunni endogenous retrovirus; MELV, Mustelidae endogenous Lentivirus; MERV-L, Murine endogenous retrovirus type L; MMLV, Moloney murine leukemia virus; MMTV, Mouse mammary tumor virus; MVV, Maedi-visna virus; PERV-A, Porcine endogenous retrovirus A; PERV-C, Porcine endogenous retrovirus C; pSIVgml, Gray mouse lemur prosimian immunodeficiency virus; Python-molurus, Python molurus endogenous retrovirus; RELIK, Rabbit endogenous lentivirus type K; RfRV, Rhinolophus ferrumequinum retrovirus; SFV, Simian foamy virus; SIV, Simian immunodeficiency virus; SloEFV, Sloth endogenous foamy virus; SnRV, Snakehead retrovirus; SRV-1, Simian retrovirus 1; SRV-2, Simian retrovirus 2; SSSV, Atlantic salmon swim bladder sarcoma virus; TTERV, Tursiops truncatus endogenous retrovirus; WDSV, Walleye dermal sarcoma virus; WEHV-1, Walleye epidermal hyperplasia virus type 1; WEHV-2, Walleye epidermal hyperplasia virus type 2; XTERV2, Xenopus tropicalis endogenous retrovirus 2; ZAERV-A, Zonotrichia albicollis endogenous retrovirus type A; ZFERV, Zebrafish endogenous retrovirus.