Mitogenomes provide insights into the phylogeny and evolution of brittle stars (Echinodermata, Ophiuroidea).

Ophiuroidea is the most speciose of all classes of Echinoderma. It is an important component in benthic ecosystems, occurring in almost all ecological niches of modern seas. To date, the phylogeny and complete evolutionary history of the ophiuroids have not yet been fully resolved. In this study, we sequenced the complete mitochondrial genomes (mitogenomes) of Ophiothrix (Ophiothrix) exigua and two deep‐sea species Histampica sp. CS049 and Ophioplinthaca sp. M5261. These two deep‐sea ophiuroids displayed reversed strand‐compositional bias and rearranged gene orders. Thirteen distinct patterns of mitochondrial gene order among ophiuroid mitogenomes were detected, with two gene order newly found in Ophiuroidea. Our data supported the gene order found in all sampled Ophiuridae as the most likely ancestral order of all Ophiuroidea. To improve phylogenetic accuracy based on nucleotide differences, two different criteria were used for the analyses: (i) nucleotide sequence from all codon positions (PCG123); (ii) the NTE method ("Neutral Transitions Excluded") for ameliorating the misleading effects of a reverse strand bias in the data. The two methods confirmed the polyphyly of the orders Ophiacanthida and Amphilepidia. At family and genus level, Ophiuridae, Ophionotus and Ophioplinthus were not monophyletic. The most notable exception was that the NTE phylogeny showed low variation of branch length. NTE dataset generated younger age for most lower‐level nodes than that from PCG123 dataset. All analyses suggested that the ophiuroids radiation occurred around the Permian–Triassic mass extinction event, and the divergence time of the deep‐sea lineages was during the Cretaceous. [ABSTRACT FROM AUTHOR]