Missing gene paralogs. (A) Summary of all newly discovered paralogs of avian missing genes, indicating copies have been independently lost in birds and mammals. Coded cells indicate genes that are present (green), missing (blue), or suspected present (light blue, gene is likely in a genomic gap). Abbreviations: Liz., lizard; N-E, non-eutherian mammal (that is, opossum and/or platypus); Hum., human; pseudo, pseudogene. (B) A maximum-likelihood phylogeny of ATP6AP-related genes based on protein alignments and rooted to deuterostomes (not shown). Branch numbers indicate bootstrap support; gene losses (in birds and mammals) are in red. Species abbreviations: Dr, Danio rerio; Mm, Mus musculus; Hs, Homo sapiens; Oa, Ornithorhynchus anatinus; Md, Monodelphis domestica; Tg, Taeniopygia gutatta; Gg, Gallus gallus; Ps, Pelodiscus sinensis; Ac, Anolis carolinensis. (C) Synteny analysis of ATP6AP1/ATP6AP1L2. The gray boxes indicate the syntenic block of genes that is deleted in birds (for example, chicken); chromosome or contig number is presented beneath each species name. (D) Examples of putative conserved functional domain analysis for paralogous gene pairs. The triangles denote predicted receptor binding sites (orange), a dimerization domain (light blue), and DNA binding sites (dark blue). Further details are in Additional file 1: Table S3. Abbreviations: AA, amino acids.