It is largely unknown how living organisms—especially vertebrates—survive and thrive in the coldness, darkness and high pressures of the hadal zone. Here, we describe the unique morphology and genome of Pseudoliparis swirei—a recently described snailfish species living below a depth of 6,000 m in the Mariana Trench. Unlike closely related shallow sea species, P. swirei has transparent, unpigmented skin and scales, thin and incompletely ossified bones, an inflated stomach and a non-closed skull. Phylogenetic analyses show that P. swirei diverged from a close relative living near the sea surface about 20 million years ago and has abundant genetic diversity. Genomic analyses reveal that: (1) the bone Gla protein (bglap) gene has a frameshift mutation that may cause early termination of cartilage calcification; (2) cell membrane fluidity and transport protein activity in P. swirei may have been enhanced by changes in protein sequences and gene expansion; and (3) the stability of its proteins may have been increased by critical mutations in the trimethylamine N-oxide-synthesizing enzyme and hsp90 chaperone protein. Our results provide insights into the morphological, physiological and molecular evolution of hadal vertebrates.

Tibetan loaches are the largest group of Tibetan fishes and are well adapted to the Tibetan Plateau. To investigate the origin of Tibetan loaches and their adaptations to the Tibetan Plateau, we determined 32 complete mitochondrial genomes that included 29 Tibetan loach species, two Barbatula species and Schistura longus. By combining these newly determined sequences with other previously published mitochondrial genomes, we assembled a large mitogenomic data set (11,433 bp) of 96 species in the superfamily Cobitoidea, to investigate the phylogenetic status of the genus Triplophysa. The resulting phylogeny strongly supported that the genus Triplophysa forms a monophyletic group within Nemacheilidae. Our molecular dating time suggests that the lineage leading to the Tibetan loaches and other loaches diverged approximately 23.5 Ma, which falls within the period of recent major uplifts of the Tibetan Plateau in the Early Miocene. Selection analyses revealed that the mitochondrial protein-coding genes of Tibetan loaches have larger ratios of nonsynonymous to synonymous substitutions than do those of non-Tibetan loaches, indicating that Tibetan loaches accumulated more nonsynonymous mutations than non-Tibetan loaches and exhibited rapid evolution. Two positively selected sites were identified in the ATP8 and ND1 genes.

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