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Research articles

Phylogeographic structure and historical demography of tarakihi (Nemadactylus macropterus) and king tarakihi (Nemadactylus n.sp.) in New Zealand

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Pages 247-271 | Received 02 Dec 2020, Accepted 27 Mar 2021, Published online: 07 Apr 2021

References

  • Aboim MA, Menezes GM, Schlitt T, Rogers AD. 2005. Genetic structure and history of populations of the deep-sea fish Helicolenus dactylopterus (Delaroche, 1809) inferred from mtDNA sequence analysis. Molecular Ecology. 14:1343–1354. DOI:10.1111/j.1365-294X.2005.02518.x.
  • Aljanabi SM, Martinez I. 1997. Universal and rapid salt-extraction of high quality genomic DNA for PCR- based techniques. Nucleic Acids Research. 25:4692–4693. DOI:10.1093/nar/25.22.4692.
  • Allendorf FW, Hohenlohe PA, Luikart G. 2010. Genomics and the future of conservation genetics. Nature Reviews Genetics. 11:697–709. DOI:10.1038/nrg2844.
  • Alloway BV, Lowe DJ, Barrell DJA, Newnham RM, Almond PC, Augustinus PC, Bertler NAN, Carter L, Litchfield NJ, McGlone MS, et al. 2007. Towards a climate event stratigraphy for New Zealand over the past 30 000 years (NZ-INTIMATE project). Journal of Quaternary Science. 22:9–35. DOI:10.1002/jqs.1079.
  • Annala JH. 1987. The biology and fishery of tarakihi, Nemadactylus macropterus, in New Zealand waters (Fisheries Research Division Occasional Publication No. 51). Wellington: New Zealand Ministry of Agriculture and Fisheries.
  • Archer FI, Adams PE, Schneiders BB. 2017. stratag : An r package for manipulating, summarizing and analysing population genetic data. Molecular Ecology Resources. 17(1):5–11. DOI:10.1111/1755-0998.12559.
  • Becker RA, Wilks AR, Brownrigg R, Minka TP, Deckmyn A. 2018. maps: draw geographical maps. https://cran.r-project.org/package=maps.
  • Beddington JR, Agnew DJ, Clark CW. 2007. Current problems in the management of marine fisheries. Science. 316:1713–1716. DOI:10.1126/science.1137362.
  • Begg GA, Friedland KD, Pearce JB. 1999. Stock identification and its role in stock assessment and fisheries management: an overview. Fisheries Research. 43:1–8. DOI:10.1016/S0165-7836(99)00062-4.
  • Benestan L. 2019. Population genomics applied to fishery management and conservation. In: Oleksiak M. Rajora O, editors. Population genomics: marine organisms. Cham: Springer; p. 399–421. DOI:10.1007/13836_2019_66
  • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B. 57:289–300. DOI:10.1111/j.2517-6161.1995.tb02031.x.
  • Bernatchez L, Wellenreuther M, Araneda C, Ashton DT, Barth JMI, Beacham TD, Maes GE, Martinsohn JT, Miller KM, Naish KA, et al. 2017. Harnessing the power of genomics to secure the future of seafood. Trends in Ecology & Evolution. 32:665–680. DOI:10.1016/j.tree.2017.06.010.
  • Birky CW, Fuerst P, Maruyama T. 1989. Organelle gene diversity under migration, mutation, and drift: equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes. Genetics. 121:613–627.
  • Bivand R, Keitt T, Rowlingson B. 2019. rgdal: Bindings for the “Geospatial” Data Abstraction Library. https://cran.r-project.org/package=rgdal.
  • Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, et al. 2019. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Computational Biology. 15:1–28. DOI:10.1371/journal.pcbi.1006650.
  • Bowen BW, Muss A, Rocha LA, Grant WS. 2006. Shallow mtDNA coalescence in Atlantic pygmy angelfishes (genus Centropyge) indicates a recent invasion from the Indian ocean. Journal of Heredity. 97(1):1–12. DOI:10.1093/jhered/esj006.
  • Brown KH. 2008. Fish mitochondrial genomics: sequence, inheritance and functional variation. Journal of Fish Biology. 72:355–374. DOI:10.1111/j.1095-8649.2007.01690.x.
  • Brown SDJ, Collins RA, Boyer S, Lefort M-C, Malumbres-Olarte J, Vink CJ, Cruickshank RH. 2012. Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding. Molecular Ecology Resources. 12:562–565. DOI:10.1111/j.1755-0998.2011.03108.x.
  • Burridge CP. 1999. Molecular phylogeny of Nemadactylus and Acantholatris (Perciformes: Cirrhitoidea: Cheilodactylidae), with implications for taxonomy and biogeography. Molecular Phylogenetics and Evolution. 13:93–109. DOI:10.1006/mpev.1999.0622.
  • Burridge CP, Smolenski AJ. 2003. Lack of genetic divergence found with microsatellite DNA markers in the tarakihi Nemadactylus macropterus. New Zealand Journal of Marine and Freshwater Research. 37:223–230. DOI:10.1080/00288330.2003.9517160.
  • Cadrin SX. 2020. Defining spatial structure for fishery stock assessment. Fisheries Research. 221:Article id 105397. DOI:10.1016/j.fishres.2019.105397.
  • Cadrin SX, Kerr LA, Mariani S. 2014. Stock identification methods: an overview. In: Cadrin S.X., Kerr L.A., Mariani S, editors. Stock identification methods: applications in fishery science. San Diego (CA): Academic Press; p. 1–5.
  • Carvalho GR, Hauser L. 1994. Molecular genetics and the stock concept in fisheries. Reviews in Fish Biology and Fisheries. 4:326–350. DOI:10.1007/BF00042908.
  • Chiswell S. 2009. Colonisation and connectivity by intertidal limpets among New Zealand, Chatham and Sub- Antarctic Islands. II. Oceanographic connections. Marine Ecology Progress Series. 388:121–135. DOI:10.3354/meps08167.
  • Chiswell SM, Bostock HC, Sutton PJH, Williams MJ. 2015. Physical oceanography of the deep seas around New Zealand: a review. New Zealand Journal of Marine and Freshwater Research. 49:286–317. DOI:10.1080/00288330.2014.992918.
  • Clarke CR, Karl SA, Horn RL, Bernard AM, Lea JS, Hazin FH, Prodöhl PA, Shivji MS. 2015. Global mitochondrial DNA phylogeography and population structure of the silky shark, Carcharhinus falciformis. Marine Biology. 162:945–955. DOI:10.1007/s00227-015-2636-6.
  • Clement M, Snell Q, Walker P, Posada D, Crandall K. 2002. TCS: estimating gene genealogies. 16th International Parallel and Distributed Processing Symposium. 2:184.
  • Darriba D, Taboada GL, Doallo R, Posada D. 2012. Jmodeltest 2: more models, new heuristics and parallel computing. Nature Methods. 9:772–772. DOI:10.1038/nmeth.2109.
  • Donaldson KA, Wilson RR. 1999. Amphi-panamic geminates of snook (Percoidei: Centropomidae) provide a calibration of the divergence rate in the mitochondrial DNA control region of fishes. Molecular Phylogenetics and Evolution. 13:208–213. DOI:10.1006/mpev.1999.0625.
  • Dray S, Dufour AB. 2007. The ade4 package: implementing the duality diagram for ecologists. Journal of Statistical Software. 22:1–20. DOI:10.18637/jss.v022.i04.
  • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research. 32:1792–1797. DOI:10.1093/nar/gkh340.
  • Elliott NG, Ward RD. 1994. Enzyme variation in jackass morwong, Nemadactylus macropterus (Schneider, 1801) (Teleostei: Cheilodactylidae), from Australian and New Zealand waters. Marine and Freshwater Research. 45:51–67. DOI:10.1071/MF9940051.
  • Excoffier L. 2015. Arlequin Ver 3.5: an integrated software package for population genetics data analysis. Swiss Institute of Bioinformatics, Bern, Switzerland. http://cmpg.unibe.ch/software/arlequin35/man/Arlequin35.pdf.
  • Excoffier L, Lischer HEL. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources. 10:564–567. DOI:10.1111/j.1755-0998.2010.02847.x.
  • Fisheries New Zealand. 2018. Fisheries assessment plenary: stock assessment and stock status volume 3: pipi to yellow-eyed mullet. Wellington: Ministry for Primary Industries.
  • Fricke R, Eschmeyer WN, Van Der Laan R. 2020. Eschmeyer’s Catalog of Fishes: genera, species, references. http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp [accessed 2020 Sep 9].
  • Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147:915–925.
  • Gauldie RW, Johnston AJ. 1980. The geographical distribution of phosphoglucomutase and glucose phosphate isomerase alleles of some New Zealand fishes. Comparative Biochemistry and Physiology Part B: Comparative Biochemistry. 66:171–183. DOI:10.1016/0305-0491(80)90051-6.
  • Grant WS, Bowen BW. 1998. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. Journal of Heredity. 89:415–426. DOI:10.1093/jhered/89.5.415.
  • Grant WS, Waples RS. 2000. Spatial and temporal scales of genetic variability in marine and anadromous species: implications for fisheries oceanography. In: Harrison PJ, Parsons TR, editors. fisheries oceanography: An integrative approach to fisheries ecology and management. Cambridge: Blackwell Science; p. 63–93.
  • Grewe PM, Smolenski AJ, Ward RD. 1994. Mitochondrial DNA diversity in jackass morwong (Nemadactylus macropterus: Teleostei) from Australian and New Zealand waters. Canadian Journal of Fisheries and Aquatic Sciences. 51:1101–1109. DOI:10.1139/f94-109.
  • Hanchet SM, Field K. 2001. Review of current and historical data for tarakihi (Nemadactylus macropterus) fishstocks TAR 1,2,3, and 7, and recommendations for future monitoring. Wellington: Ministry of Fisheries.
  • Harpending HC. 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Human Biology. 66:591–600.
  • Harrison RG. 1989. Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends in Ecology & Evolution. 4:6–11. DOI:10.1016/0169-5347(89)90006-2.
  • Hauser L, Adcock GJ, Smith PJ, Bernal Ramírez JH, Carvalho GR. 2002. Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proceedigns of the National Academy of Sciences of the United States of America. 99:11742–11747. DOI:10.1073/pnas.172242899.
  • Hewitt G. 2000. The genetic legacy of the quaternary ice ages. Nature. 405:907–913. DOI:10.1038/35016000.
  • Hewitt GM. 2004. Genetic consequences of climatic oscillations in the quaternary. Philosophical Transactions of the Royal Society B: Biological Sciences. 359:183–195. DOI:10.1098/rstb.2003.1388.
  • Hickey AJR, Lavery SD, Hannan DA, Baker CS, Clements KD. 2009. New Zealand triplefin fishes (family tripterygiidae): contrasting population structure and mtDNA diversity within a marine species flock. Molecular Ecology. 18:680–696. DOI:10.1111/j.1365-294X.2008.04052.x.
  • Jombart T. 2008. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics. 24:1403–1405. DOI:10.1093/bioinformatics/btn129.
  • Kaschner K, Kesner-Reyes K, Garilao C, Segschneider J, Rius-Barile J, Rees T, Froese R. 2019. AquaMaps: Predicted range maps for aquatic species version 10/2019. [accessed 2021 Feb 17]. www.aquamaps.org.
  • Kimura K, Imamura H, Kawai T. 2018. Comparative morphology and phylogenetic systematics of the families Cheilodactylidae and Latridae (Perciformes: Cirrhitoidea), and proposal of a new classification. Zootaxa. 4536:1–72. DOI:10.11646/zootaxa.4536.1.1.
  • Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution. 33:1870–1874. DOI:10.1093/molbev/msw054.
  • Laikre L, Palm S, Ryman N. 2005. Genetic population structure of fishes: implications for coastal zone management. AMBIO: A Journal of the Human Environment. 34:111–119. DOI:10.1579/0044-7447-34.2.111.
  • Lane HS, Symonds JE, Ritchie PA. 2016. The phylogeography and population genetics of Polyprion oxygeneios based on mitochondrial DNA sequences and microsatellite DNA markers. Fisheries Research. 174:19–29. DOI:10.1016/j.fishres.2015.08.009.
  • Langley AD. 2018. Stock assessment of tarakihi off the east coast of mainland New Zealand (New Zealand Fisheries Assessment Report 2018/05). Ministry for Primary Industries, Wellington, New Zealand.
  • Lee W-J, Conroy J, Howell WH, Kocher T. 1995. Structure and evolution of teleost mitochondrial control regions. Journal of Molecular Evolution. 41:54–66. DOI:10.1007/BF00174041.
  • Lévy-Hartmann L, Roussel V, Letourneur Y, Sellos DY. 2011. Global and New Caledonian patterns of population genetic variation in the deep-sea splendid alfonsino, Beryx splendens, inferred from mtDNA. Genetica. 139:1349–1365. DOI:10.1007/s10709-012-9628-y.
  • Ludt WB, Burridge CP, Chakrabarty P. 2019. A taxonomic revision of Cheilodactylidae and Latridae (centrarchiformes: cirrhitoidei) using morphological and genomic characters. Zootaxa. 4585:121–141. DOI:10.11646/zootaxa.4585.1.7.
  • Machado RC, da Silva Cortinhas MC, Proietti MC, Haimovici M. 2020. Genetic connectivity of black drum (Pogonias courbina) stocks in the southwestern Atlantic Ocean. Environmental Biology of Fishes. 103:913–926. DOI:10.1007/s10641-020-00993-6.
  • McKenzie JR, Beentjes M, Parker S, Parsons DM, Armiger H, Wilson O, Middleton D, Langley A, Buckthought D, Walsh C, et al. 2017. Fishery characterisation and age composition of tarakihi in TAR 1, 2 and 3 for 2013/14 and 2014/15 (New Zealand Fisheries Assessment Report 2017/36). Wellington: Ministry for Primary Industries.
  • McSaveney E. 2007. Glaciers and glaciation – The ice ages. Te Ara – Encycl. New Zeal. http://www.teara.govt.nz/en/diagram/10741/glacial-periods-in-new-zealand [accessed 2020 Sep 14].
  • Meirmans PG. 2015. Seven common mistakes in population genetics and how to avoid them. Molecular Ecology. 24(13):3223–3231. DOI:10.1111/mec.13243.
  • Morrison MA, Jones EG, Parsons DP, Grant CM. 2014. Habitats and areas of particular significance for coastal finfish fisheries management in New Zealand: A review of concepts and life history knowledge, and suggestions for future research (New Zealand Aquatic Environment and Biodiversity Report No. 125). Wellington: Ministry for Primary Industries.
  • Ovenden JR, Berry O, Welch DJ, Buckworth RC, Dichmont CM. 2015. Ocean’s eleven: A critical evaluation of the role of population, evolutionary and molecular genetics in the management of wild fisheries. Fish and Fisheries. 16:125–159. DOI:10.1111/faf.12052.
  • Ovenden JR, Leigh GM, Blower DC, Jones AT, Moore A, Bustamante C, Buckworth RC, Bennett MB, Dudgeon CL. 2016. Can estimates of genetic effective population size contribute to fisheries stock assessments? Journal of Fish Biology. 89:2505–2518. DOI:10.1111/jfb.13129.
  • Papa Y, Oosting T, Valenza-Troubat N, Wellenreuther M, Ritchie PA. 2021. Genetic stock structure of New Zealand fish and the use of genomics in fisheries management: an overview and outlook. New Zealand Journal of Zoology. 48(1):1–31. DOI:10.1080/03014223.2020.1788612.
  • Paradis E, Schliep K. 2018. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics. 35:526–528. DOI:10.1093/bioinformatics/bty633.
  • Pinsky ML, Palumbi SR. 2014. Meta-analysis reveals lower genetic diversity in overfished populations. Molecular Ecology. 23:29–39. DOI:10.1111/mec.12509.
  • Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. 2018. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67:901–904. DOI:10.1093/sysbio/syy032.
  • R Core Team. 2020. R: A language and environment for statistical computing. R Found. Stat. Comput., Vienna, Austria.
  • Reiss H, Hoarau G, Dickey-Collas M, Wolff WJ. 2009. Genetic population structure of marine fish: mismatch between biological and fisheries management units. Fish and Fisheries. 10:361–395. DOI:10.1111/j.1467-2979.2008.00324.x.
  • Roberts CD, Stewart AL, Struthers CD. 2015. The fishes of New Zealand. Wellington: Te Papa Press.
  • Roberts CD, Stewart AL, Struthers CD, Barker JJ, Kortet S. 2020. Checklist of the fishes of New Zealand. Online version 1.2. Wellington: Museum of New Zealand Te Papa Tongarewa. https://collections.tepapa.govt.nz/document/10564.
  • Rogers AR, Harpending H. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution. 9:552–569. DOI:10.1093/oxfordjournals.molbev.a040727.
  • Ross PM, Hogg ID, Pilditch CA, Lundquist CJ. 2009. Phylogeography of New Zealand’s coastal benthos. New Zealand Journal of Marine and Freshwater Research. 43:1009–1027. DOI:10.1080/00288330.2009.9626525.
  • Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evoluation. 34:3299–3302. DOI:10.1093/molbev/msx248.
  • RStudio Team. 2020. RStudio: integrated development environment for R. Boston (MA): RStudio, PBC.
  • Sanger F, Nicklen S, Coulson AR. 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America. 74:5463–5467. DOI:10.1073/pnas.74.12.5463.
  • Shulmeister J, Thackray GD, Rittenour TM, Fink D, Patton NR. 2019. The timing and nature of the last glacial cycle in New Zealand. Quaternary Science Reviews. 206:1–20. DOI:10.1016/j.quascirev.2018.12.020.
  • Smith HM. 2012. Characterisation of the mitochondrial genome and the phylogeographic structure of blue cod (Parapercis colias) [master’s thesis]. Victoria University of Wellington, New Zealand.
  • Smith PJ, Paulin CD. 2003. Genetic and morphological evidence for a single species of pink ling (Genypterus blacodes) in New Zealand waters. New Zealand Journal of Marine and Freshwater Research. 37:183–194. DOI:10.1080/00288330.2003.9517156.
  • Smith PJ, Roberts CD, McVeagh SM, Benson PG. 1996. Genetic evidence for two species of tarakihi (Teleostei: Cheilodactylidae: Nemadactylus) in New Zealand waters. New Zealand Journal of Marine and Freshwater Research. 30:209–220. Doi:10.1080/00288330.1996.9516709.
  • Smith PJ, Steinke D, Mcmillan PJ, Mcveagh SM, Struthers CD. 2008. DNA database for commercial marine fish (New Zealand Aquatic Environment and Biodiversity Report No. 22). Wellington: Ministry of Fisheries.
  • Suggate RP. 1990. Late pliocene and quaternary glaciations of New Zealand. Quaternary Science Reviews. 9:175–197. DOI:10.1016/0277-3791(90)90017.
  • Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123:585–595.
  • Tong LJ, Vooren CM. 1972. The biology of the New Zealand tarakihi, Cheilodactylus macropterus (Bloch and Schneider). Wellington: New Zealand Ministry of Agriculture and Fisheries.
  • van Etten J.. 2017. R package gdistance: Distances and routes on geographical grids. Journal of Statistical Software. 76:1–21. DOI:10.18637/jss.v076.i13.
  • von der Heyden S, Lipinski MR, Matthee CA. 2010. Remarkably low mtDNA control region diversity in an abundant demersal fish. Molecular Phylogenetics and Evolution. 55(3):1183–1188. DOI:10.1016/j.ympev.2009.09.018.
  • Wallis GP, Trewick SA. 2009. New Zealand phylogeography: evolution on a small continent. Molecular Ecology. 18:3548–3580. DOI:10.1111/j.1365-294X.2009.04294.x.
  • Waples RS. 1998. Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. Journal of Heredity. 89(5):438–450. DOI:10.1093/jhered/89.5.438.
  • Waples RS, Punt AE, Cope JM. 2008. Integrating genetic data into management of marine resources: How can we do it better? Fish and Fisheries. 9:423–449. DOI:10.1111/j.1467-2979.2008.00303.x.
  • Wickham H. 2009. Ggplot2: elegant graphics for data analysis. 1st ed. New York (NY): Springer.
  • Xiao Y, Zhang Y, Gao T, Yanagimoto T, Yabe M, Sakurai Y. 2009. Genetic diversity in the mtDNA control region and population structure in the small yellow croaker Larimichthys polyactis. Environmental Biology of Fishes. 85:303–314. DOI:10.1007/s10641-009-9497-0.

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