Mitochondrial genome of the jack silverside, Atherinopsis californiensis (Atherinopsidae, Atheriniformes), a nearshore fish of the California Current Ecosystem

References

• Allen LG, Pondella II, DJ. 2006. Surf zone, coastal pelagic zone, and harbors. In: Allen LG, Pondella II, DJ, Horn MH, editors. The ecology of marine fishes: california and adjacent waters. Berkeley, (CA): University of California Press; p. 149–166.
   Google Scholar
• Alqahtani F, Mandoiu I. 2020. SMART2: multi-library statistical mitogenome assembly with repeats. In: Mandoiu I, Murali T, Narasimhan G, Rajasekaran S, Skums S, Zelikovsky A, editors. Computational advances in bio and medical sciences. Lecture notes in bioinformatics. Vol. 12029. Cham, Switzerland: Springer.
   Google Scholar
• Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
   Google Scholar
• Barriga-Sosa IDLA, García De León FJ, Del Río-Portilla MA. 2016. The complete mitochondrial DNA of the endemic shortfin silverside, Chirostoma humboldtianum (Valenciennes, 1835). Mitochondrial DNA A DNA Mapp Seq Anal. 27(2):1545–1546.
   PubMedGoogle Scholar
• Barry JP, Yoklavich MM, Cailliet GM, Ambrose DA, Antrim BS. 1996. Trophic ecology of the dominant fishes in Elkhorn Slough, California, 1974–1980. Estuaries. 19(1):115–138.
   Google Scholar
• Bloom DD, Unmack PJ, Gosztonyi AE, Piller KR, Lovejoy NR. 2012. It’s a family matter: molecular phylogenetics of Atheriniformes and the polyphyly of the surf silversides (Family: notocheiridae). Mol Phylogenet Evol. 62(3):1025–1030.
   PubMed Web of Science ®Google Scholar
• Chen S, Zhou Y, Chen Y, Gu J. 2018. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 34(17):i884–i890.
   PubMed Web of Science ®Google Scholar
• Clark FN. 1929. Fish Bulletin No. 16: the life history of the California jack smelt, Atherinopsis californiensis. Division of Fish and Game of California. 23 p.
   Google Scholar
• Closek CJ, Santora JA, Starks HA, Schroeder ID, Andruszkiewicz EA, Sakuma KM, Bograd SJ, Hazen EL, Field JC, Boehm AB. 2019. Marine vertebrate biodiversity and distribution within the central California Current using environmental DNA (eDNA) metabarcoding and ecosystem surveys. Front Mar Sci. 6:732.
   Web of Science ®Google Scholar
• Crabtree CB. 1987. Allozyme evidence for the phylogenetic relationships within the silverside subfamily Atherinopsinae. Copeia. 1987(4):860–867.
   Google Scholar
• De La Cruz-Agüero J, Galvan-Magana F, Abitia-Cardenas LA, Rodriquez-Romero J, Gutierrez-Sanchez FJ. 1994. Systematic list of marine fishes from Bahia Magdalena, Baja California Sur (Mexico). Ciencias Mar. 20:17–31.
   Google Scholar
• Higgins BA, Horn MH. 2014. Suction among pickers: jaw mechanics, dietary breadth and feeding behaviour in beach-spawning Leuresthes spp. compared with their relatives. J Fish Biol. 84(6):1689–1707.
   PubMed Web of Science ®Google Scholar
• Hill KT, Schneider N. 1999. Historical logbook databases from California’s commercial passenger fishing vessel (partyboat) fishery, 1936–1997. San Diego (CA): University of California, Scripps Institution of Oceanography Ref. Ser. No. 99–19.
   Google Scholar
• Horn MH, Gawlicka AK, German DP, Logothetis EA, Cavanagh JW, Boyle KS. 2006. Structure and function of the stomachless digestive system in three related species of New World silverside fishes (Atherinopsidae) representing herbivory, omnivory, and carnivory. Mar Biol. 149(5):1237–1245.
   Web of Science ®Google Scholar
• Horn MH. 1979. Diel and seasonal variation in abundance and diversity of shallow-water fish populations in Morro Bay. California Fish Bull. 78:759–770.
   Web of Science ®Google Scholar
• Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M, et al. 2013. MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol. 30(11):2531–2540.
   PubMed Web of Science ®Google Scholar
• Jarvis ET, Allen MJ, Smith RW. 2004. Comparison of recreational fish Catch trends to environment-species relationships and fishery-independent data in the Southern California Bight, 1980–2000. California Cooperat Ocean Fish Invest Rep. 45:167.
   Web of Science ®Google Scholar
• Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods. 9(4):357–359.
   PubMed Web of Science ®Google Scholar
• Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics. 23(21):2947–2948.
   PubMed Web of Science ®Google Scholar
• Lewis OH, Lema SC. 2019. Sequence and phylogenetic analysis of the mitochondrial genome for the Northern Anchovy, Engraulis mordax (Engraulidae: clupeiformes). Mitochondrial DNA B Resour. 4(1):14–16.
   PubMed Web of Science ®Google Scholar
• Lin M, Mu X, Yan X. 2017. The complete mitochondrial genome of Cichla ocellaris. Mitochondrial DNA B Resour. 2(2):620–622.
   PubMed Web of Science ®Google Scholar
• Lou RN, Fletcher NK, Wilder AP, Conover DO, Therkildsen NO, Searle JB. 2018. Full mitochondrial genome sequences reveal new insights about post-glacial expansion and regional phylogeographic structure in the Atlantic silverside (Menidia menidia). Mar Biol. 165(8):1–18.
   Web of Science ®Google Scholar
• Lü Z, Zhu K, Liu L, Liu B, Jiang L, Gong L. 2018. Phylogenetic analysis of the complete mitochondrial genome of Hyporhamphus limbatus (Beloniformes; hemiramphidae). Mitochondrial DNA B Resour. 3(2):1292–1293.
   PubMed Web of Science ®Google Scholar
• Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, et al. 2003. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol. 26(1):121–138.
   PubMed Web of Science ®Google Scholar
• Muñoz NC, Dickson KA, Walter RP. 2020. The mitogenome of the California grunion (Leuresthes tenuis). Mitochondr DNA B. 5(2):1138–1140.
   Web of Science ®Google Scholar
• Ono DS. 1982. Southern California marine sport fishing from privately owned boats: catch and effort for January–March 1982. Marine Resources Administrative Report 82–12. Sacramento (CA): California Department of Fish and Game.
   Google Scholar
• Sato Y, Miya M, Fukunaga T, Sado T, Iwasaki W. 2018. MitoFish and MiFish pipeline: a mitochondrial genome database of fish with an analysis pipeline for environmental DNA metabarcoding. Mol Biol Evol. 35(6):1553–1555.
   PubMed Web of Science ®Google Scholar
• Setiamarga DHE, Miya M, Yamanoue Y, Mabuchi K, Satoh TP, Inoue JG, Nishida M. 2008. Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): The first evidence based on whole mitogenome sequences. Mol Phylogenet Evol. 49(2):598–605.
   PubMed Web of Science ®Google Scholar
• Stat M, John J, DiBattista JD, Newman SJ, Bunce M, Harvey ES. 2019. Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity. Conserv Biol. 33(1):196–205.
   PubMed Web of Science ®Google Scholar
• Stothard P, Wishart DS. 2005. Circular genome visualization and exploration using CGView. Bioinformatics. 21(4):537–539.
   PubMed Web of Science ®Google Scholar
• Tamura K, Stecher G, Kumar S. 2021. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol. 38(7):3022–3027.
   PubMed Web of Science ®Google Scholar
• Zhu K, Lü Z, Liu B, Gong L, Jiang L, Liu L. 2018. The complete mitochondrial genome of Hyporhamphus quoyi (Beloniformes; Hemiramphidae). Mitochondrial DNA B Resour. 3(2):1235–1236.
   PubMed Web of Science ®Google Scholar