Although aerobic respiration is a hallmark of eukaryotes, a few unicellular lineages, growing in hypoxic environments, have secondarily lost this ability. In the absence of oxygen, the mitochondria of these organisms have lost all or parts of their genomes and evolved into mitochondria related organelles (MROs). There has been debate regarding the presence of MROs in animals. Using deep sequencing approaches, we discovered that a member of the Cnidaria, the myxozoan Henneguya salminicola, has no mitochondrial genome, and thus has lost the ability to perform aerobic cellular respiration. This is the only animal described without these core eukaryotic features. Our analyses suggest that H. salminicola lost not only its mitochondrial genome, but also nearly all nuclear genes involved in transcription and replication of the mitochondrial genome. In contrast, we identified many genes that encode proteins involved in other mitochondrial pathways and determined that genes involved in aerobic respiration or mitochondrial DNA replication were either absent, or present only as pseudogenes. As a control, we used the same sequencing and annotation methods to show that the closely-related myxozoan, Myxobolus squamalis, has a mitochondrial genome. The molecular results are supported by fluorescence micrographs, which show the presence of mitochondrial DNA in M. squamalis but not in H. salminicola. Our discovery confirms that adaptation to an anaerobic environment is not unique to single-celled eukaryotes but has also evolved in a multicellular, parasitic animal. Hence, H. salminicola provides an opportunity for understanding the evolutionary transition from an aerobic to an exclusive anaerobic metabolism.

Two matrices were selected from a database of 78 ribosomal protein coding genes, which has been curated manually to avoid contamination and structural annotation errors. The first dataset included 78 species representative of major eukaryote lineages; the second included 129 species that encompassed animal diversity and their closest outgroup (choanoflagellates, ichthyosporean and ministeriid). In both datasets, sequences were concatenated with SCaFoS. After removal of any ambiguously aligned positions using Gblocks Version 0.91b, with default parameter values, these Eukaryote and Metazoa datasets included 9,490 and 11,352 amino acid positions, respectively. Phylogenetic reconstructions were performed using the site-heterogeneous CAT model, which reduces the impact of long branch attraction, as implemented in Phylobayes MPI vs.1.5. For both datasets, two independent chains were run for 10,000 cycles. The first 5,000 trees from each chain were discarded as burn-in. Chain convergence was assessed using the bpcomp and tracecomp scripts which are part of Phylobayes. Specifically, for both analyses the bpcomp maxdiff values were <0.3 and the tracecomp effsize values were >70 (except for eukaryotes where the tree length value was 21), indicating a proper convergence.

The trees are in Newick format.

The matrices are in Nexus format, the different gene partitions are indicated in the "Set Block" (under the matrix).