Carr S. M. 2023 Things fall apart: multiple mitogenomes provide an alternative evolutionary phylogeography to thrice out of Africa or Asia hypotheses for Western honey bees (Apis mellifera). Nat. Sci. Rep. 13, 9386–9398

CAS  Google Scholar 

Chan P. P., Lin B. Y., Mak A. J. and Lowe T. M. 2021 tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res. 49, 9077–9096

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dierckxsens N., Mardulyn P. and Smits G. 2017 NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45, e18

PubMed  Google Scholar 

Feng S. X., Wang X., Zhang Y., Qin G., Lin Q. and Zhang Y. H. 2023 Genetic basis of embryo and juvenile physiological responses to salinity changes in freshwater pipefish (Hippichthys heptagonus). Zool Res. 44, 743–746

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hillis D. M. 1987 Molecular versus morphological approaches to systematics. Annu. Rev. Ecol. Syst. 18, 23–42

Article  Google Scholar 

Minh B. Q., Schmidt H. A., Chernomor O., Schrempf D., Woodhams M. D., von Haeseler A. et al. 2020 IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534

Article  CAS  PubMed  PubMed Central  Google Scholar 

Moritz C. 1994 Applications of mitochondrial DNA analysis in conservation: a critical review. Mol. Ecol. 3, 401–411

Article  CAS  Google Scholar 

Noack K., Zardoya R. and Meyer A. 1996 The complete mitochondrial DNA sequence of the bichir (Polypterus ornatipinnis), a basal ray-finned fish: ancient establishment of the consensus vertebrate gene order. Genetics 144, 1165–1180

Article  CAS  PubMed  PubMed Central  Google Scholar 

Peng Z., Wang J. and He S. 2006 The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene 376, 290–297

Article  CAS  PubMed  Google Scholar 

Ronquist F., Teslenko M., van der Mark P., Ayres D. L., Darling A., Höhna S. et al. 2012 MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542

Article  PubMed  PubMed Central  Google Scholar 

Stiller J., Short G., Hamilton H., Saarman N., Longo S., Wainwright P. et al. 2022 Phylogenomic analysis of Syngnathidae reveals novel relationships origins of endemic diversity and variable diversification rates. BMC Biol. 20, 75

Article  PubMed  PubMed Central  Google Scholar 

Wiley E. O. and Mayden R. L. 1985 Species and speciation in phylogenetic systematics, with examples from the North American fish fauna. Ann. Mol. Bot. Gard. 72, 596–635

Article  Google Scholar 

Yang B., Wang Y. and Qian P. Y. 2016 Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis. BMC Bioinform. 17, 1–8

Article  CAS  Google Scholar 

Zhang D., Gao F., Jakovlić I., Zou H., Zhang J., Li W. X. et al. 2020 PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol. Ecol. Resour. 20, 348–355

Article  PubMed  Google Scholar 

Zhang Y., Zhang H., Lin Q. and Huang L. 2015 Complete mitochondrial genome sequence of the lined seahorse Hippocampus erectus Perry, 1810 (Gasterosteiformes: Syngnathidae). Mitochondrial DNA 26, 659–660

Article  CAS  PubMed  Google Scholar 

Zhu T., Sato Y., Sado T., Miya M. and Iwasaki W. 2023 MitoFish, MitoAnnotator, and MiFish Pipeline: updates in 10 years. Mol. Biol. Evol. 40, msad035

Article  CAS  PubMed  PubMed Central  Google Scholar