The mitochondrial genomes of the reef-dwelling spiny lobsters Panulirus echinatus and Panulirus interruptus with insights into the phylogeny and adaptive evolution of protein-coding genes in the Achelata

• Published in: Coral reefs 2024-12, Vol.43 (6), p.1857-1877
• Main Authors: Baker, Alyssa M., Stephens, Natalie C., Diniz, Fabio Mendonca, León, F. J. García-de, Baeza, J. Antonio
• Format: Article
• Language: English
• Subjects: Achelata; Aquatic crustaceans; Biomedical and Life Sciences; Codification; Crustaceans; Deep water; Electron transport chain; Environmental conditions; Environmental management; Evolution; Evolution & development; Evolutionary conservation; Evolutionary genetics; Fisheries; Freshwater & Marine Ecology; Genes; Genomes; High temperature; Latitude; Life Sciences; Lobsters; Marine crustaceans; Marine invertebrates; Mitochondria; Oceanography; Oxidative phosphorylation; Oxygen; Palinuridae; Panulirus; Panulirus echinatus; Phosphorylation; Phylogeny; Positive selection; Proteins; Scyllaridae; Shellfish; Signatures
• ISSN: 0722-4028; 1432-0975
• DOI: 10.1007/s00338-024-02569-7

Temperature and oxygen levels drive the evolution of morphological, behavioral, and physiological traits in marine invertebrates, including crustaceans. Environmental conditions are also expected to prompt the adaptive evolution of mitochondrial protein-coding genes (PCGs), which are vital for energy production via the oxidative phosphorylation pathway. We formally tested for adaptive evolution in mitochondrial protein-coding genes in representatives of the decapod infraorder Achelata, including two spiny lobsters, Panulirus echinatus and P. interruptus , for which we sequenced complete mitochondrial genomes (15,644 and 15,659 bp long, respectively). A phylomitogenomic analysis supported the monophyly of the genus Panulirus , the families Palinuridae and Scyllaridae, and the infraorder Achelata. Over the strong negative selection background observed for mitochondrial PCGs in the Achelata, signatures of positive selective pressure were detected within PCGs in equatorial Panulirus spp. and deepwater Scyllaridae. In Panulirus spp. inhabiting equatorial latitudes with consistently high temperatures, the Datamonkey analysis RELAX suggested intensified purifying selection strength in 9 of the 13 PCGs and relaxation in purifying selection strength in atp6 , while aBSREL, BUSTED, and MEME recovered signatures of positive selection on PCGs within Complex I, III, and IV PCGs. Likewise, in Scyllaridae species inhabiting depths with low-oxygen levels, RELAX indicated relaxed selection strength in 6 of the 13 PCGs, while aBSREL, BUSTED, and MEME recovered signatures of positive selection on PCGs within Complexes I, III, IV, and V. The newly assembled mitochondrial genomes of P. echinatus and P. interruptus represent new genomic resources to aid with the conservation and management of lobsters targeted by major fisheries and contribute to our understanding of how environmental conditions drive adaptive evolution in spiny and slipper lobster mitochondrial PCGs.