Metabarcoding of marine zooplankton in South Africa

References

• Aylagas E, Borja Á, Rodríguez-Ezpeleta N. 2014. Environmental status assessment using DNA metabarcoding: towards a genetics-based marine biotic index (gAMBI). PLoS ONE 9: e90529.
   PubMed Web of Science ®Google Scholar
• Berry PF. 1974. Palinurid and Scyllarid lobster larvae of the Natal Coast, South Africa. Investigational Report No. 34. Durban, South Africa: Oceanographic Research Institute.
   Google Scholar
• Bezeng BS, van der Bank HF. 2019. DNA barcoding of southern African crustaceans reveals a mix of invasive species and potential cryptic diversity. PLoS ONE 14: e0222047.
   PubMed Web of Science ®Google Scholar
• Blaxter M. 2003. Molecular systematics – counting angels with DNA. Nature 421: 122–124.
   PubMed Web of Science ®Google Scholar
• Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA et al. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37: 848–857.
   PubMed Web of Science ®Google Scholar
• Bradford-Grieve JM, Blanco-Bercial L, Prusova I. 2017. Calanoides natalis Brady, 1914 (Copepoda: Calanoida: Calanidae): identity and distribution in relation to coastal oceanography of the eastern Atlantic and western Indian Oceans. Journal of Natural History 51: 807–836.
   Web of Science ®Google Scholar
• Branch GM, Griffiths CL, Branch ML, Beckley LE. 2010. Two oceans: a guide to the marine life of southern Africa. Cape Town, South Africa: Struik.
   Google Scholar
• Brierley AS. 2017. Plankton. Current Biology 27: R478–R483.
   PubMed Web of Science ®Google Scholar
• Bucklin A, Wiebe PH, Smolenack SB, Copley NJ, Beaudet JG, Bonner KG et al. 2007. DNA barcodes for species identification of euphausiids (Euphausiacea, Crustacea). Journal of Plankton Research 29: 483–493.
   Web of Science ®Google Scholar
• Bucklin A, Steinke D, Blanco-Bercial L. 2011. DNA barcoding of marine metazoa. Annual Review of Marine Science 3: 471–508.
   PubMed Web of Science ®Google Scholar
• Bucklin A, Lindeque PK, Rodriguez-Ezpeleta N, Albaina A, Lehtiniemi M. 2016. Metabarcoding of marine zooplankton: prospects, progress and pitfalls. Journal of Plankton Research 38: 393–400.
   Web of Science ®Google Scholar
• Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. 2016. DADA2: high-resolution sample inference from Illumina amplicon data. Nature Methods 13: 581–583.
   PubMed Web of Science ®Google Scholar
• Carroll EL, Gallego R, Sewell MA, Zeldis J, Ranjard L, Ross HA et al. 2019. Multi-locus DNA metabarcoding of zooplankton communities and scat reveal trophic interactions of a generalist predator. Scientific Reports 9: article 281.
   Web of Science ®Google Scholar
• Casas L, Pearman JK, Irigoien X. 2017. Metabarcoding reveals seasonal and temperature-dependent succession of zooplankton communities in the Red Sea. Frontiers in Marine Science 4: article 241.
   Web of Science ®Google Scholar
• Chamberlain S. 2018. bold: Interface to Bold Systems API. Available at https://rdrr.io/cran/bold/ [accessed January 2018].
   Google Scholar
• Cristescu ME. 2014. From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity. Trends in Ecology and Evolution 29: 566–571.
   PubMed Web of Science ®Google Scholar
• DAFF (Department of Agriculture, Forestry and Fisheries). 2016. Status of the South African marine fishery resources 2016. Cape Town, South Africa: DAFF. Available at https://www.environment.gov.za/sites/default/files/reports/statusofsouthafrican_marinefisheryresources2016.pdf.
   Google Scholar
• da Silva JM, Willows-Munro S. 2016. A review of over a decade of DNA barcoding in South Africa: a faunal perspective. African Zoology 51: 1–12.
   Web of Science ®Google Scholar
• Djurhuus A, Pitz K, Sawaya NA, Rojas-Márquez J, Michaud B, Montes E et al. 2018. Evaluation of marine zooplankton community structure through environmental DNA barcoding. Limnology and Oceanography: Methods 16: 209–221.
   PubMed Web of Science ®Google Scholar
• Dormontt EE, van Dijk K, Bell KL, Biffin E, Breed MF, Byrne M et al. 2018. Advancing DNA barcoding and metabarcoding applications for plants requires systematic analysis of herbarium collections – an Australian perspective. Frontiers in Ecology and Evolution 6: article 134.
   Web of Science ®Google Scholar
• Fisher R, Radford BT, Knowlton N, Brainard RE, Michaelis FB, Caley MJ. 2010. Global mismatch between research effort and conservation needs of tropical coral reefs. Conservation Letters 4: 64–72.
   Web of Science ®Google Scholar
• Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3: 294–299.
   PubMedGoogle Scholar
• Francis CM, Borisenko AV, Ivanova NV, Eger JL, Lim BK, Guillén-Servent A et al. 2010. The role of DNA barcodes in understanding and conservation of mammal diversity in Southeast Asia. PLoS ONE 5: e12575.
   PubMed Web of Science ®Google Scholar
• Goetze E. 2010. Species discovery in marine planktonic invertebrates through global molecular screening. Molecular Ecology 19: 952–967.
   PubMed Web of Science ®Google Scholar
• Govender A. 2021. DNA metabarcoding of zooplankton enhances community-level analyses of connectivity in a marine pelagic environment. PhD thesis, University of KwaZulu-Natal, South Africa.
   Google Scholar
• Govender A, Groeneveld J, Singh S, Willows-Munro S. 2019. The design and testing of mini-barcode markers in marine lobsters. PLoS ONE 14: e0210492
   PubMed Web of Science ®Google Scholar
• Greene CH, Pershing AJ. 2012. Climate drives sea change. Science 315: 1084–1085.
   Google Scholar
• Griffiths CL, Robinson TB. 2016. Use and usefulness of measures of marine endemicity in South Africa. South African Journal of Science 112: article 2015-0249.
   Web of Science ®Google Scholar
• Griffiths CL, Robinson TB, Lange L, Mead A. 2010. Marine biodiversity in South Africa: an evaluation of current states of knowledge. PLoS ONE 5: e12008.
   PubMed Web of Science ®Google Scholar
• Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN. 2006. DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences of the United States of America 103: 968–971.
   PubMed Web of Science ®Google Scholar
• Hays GC, Richardson AJ, Robinson C. 2005. Climate change and marine plankton. Trends in Ecology and Evolution 20: 337–344.
   PubMed Web of Science ®Google Scholar
• Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences 270: 313–321.
   PubMed Web of Science ®Google Scholar
• Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. 2004. Identification of birds through DNA barcodes. PLoS Biology 2: e312.
   PubMed Web of Science ®Google Scholar
• Hirai J, Tachibana A, Tsuda A. 2020. Large-scale metabarcoding analysis of epipelagic and mesopelagic copepods in the Pacific. PLoS ONE 15: e0233189.
   PubMed Web of Science ®Google Scholar
• Höring F, Cornils A, Auel H, Bode M, Held C. 2017. Population genetic structure of Calanoides natalis (Copepoda, Calanoida) in the eastern Atlantic Ocean and Benguela upwelling system. Journal of Plankton Research 39: 618–630.
   Google Scholar
• Huggett JA, Verheye HM, Escribano R, Fairweather T. 2009. Copepod biomass, size composition and production in the Southern Benguela: spatio-temporal patterns of variation, and comparison with other eastern boundary upwelling systems. Progress in Oceanography 83: 197–207.
   Web of Science ®Google Scholar
• Hutchings L, Jarre A, Lamont T, van den Berg M, Kirkman SP. 2012. St Helena Bay (southern Benguela) then and now: muted climate signals, large human impact. African Journal of Marine Science 34: 559–583.
   Web of Science ®Google Scholar
• Jarre A, Hutchings L, Kirkman SP, Kreiner A, Tchipalanga PCM, Kainge P et al. 2015. Synthesis: climate effects on biodiversity, abundance and distribution of marine organisms in the Benguela. Fisheries Oceanography 24: 122–149.
   Web of Science ®Google Scholar
• Ko HL, Wang YT, Chiu TS, Lee MA, Leu MY, Chang KZ et al. 2013. Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding. PLoS ONE 8: e53451.
   PubMed Web of Science ®Google Scholar
• Knolt KE, Balser EJ, Jaeckle WB, Wray GA. 2003. Identification of asteroid genera with species capable of larval cloning. Biological Bulletin 204: 246–255.
   PubMed Web of Science ®Google Scholar
• Laakmann S, Blanco-Bercial L, Cornils A. 2020. The crossover from microscopy to genes in marine diversity: from species to assemblages in marine pelagic copepods. Philosophical Transactions of the Royal Society B: Biological Sciences 375: 20190446.
   PubMed Web of Science ®Google Scholar
• Leis JM. 2015. Taxonomy and systematics of larval Indo-Pacific fishes: a review of progress since 1981. Ichthyological Research 62: 9–28.
   Web of Science ®Google Scholar
• Leray M, Knowlton N. 2015. DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proceedings of the National Academy of Sciences of the United States of America 112: 2076–2081.
   PubMed Web of Science ®Google Scholar
• Leray M, Knowlton N. 2016. Censusing marine eukaryotic diversity in the twenty-first century. Philosophical Transactions of the Royal Society B: Biological Sciences 371: 20150331.
   PubMed Web of Science ®Google Scholar
• Leray M, Yang JY, Meyer CP, Mills SC, Agudelp N, Ranwez V et al. 2013. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Frontiers in Zoology 10: article 34.
   PubMed Web of Science ®Google Scholar
• Leray M, Ho SL, Lin IJ, Machida RJ. 2018. MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database. Bioinformatics 34: 3753–3754.
   PubMed Web of Science ®Google Scholar
• Lindeque PK, Parry HE, Harmer RA, Somerfield PJ, Atkinson A. 2013. Next generation sequencing reveals the hidden diversity of zooplankton assemblages. PLoS ONE 8: e81327.
   PubMedGoogle Scholar
• Marine Zooplankton Colloquium. 2001. Future marine zooplankton research – a perspective. Marine Ecology Progress Series 222: 297–308.
   Web of Science ®Google Scholar
• Matsuda H, Sakai M, Yanagimoto T, Chow S. 2019. Morphological differences among phyllosoma larvae of the pronghorn spiny lobster, Panulirus penicillatus, from the western, central, and eastern areas of the Pacific Ocean. Crustacean Research 48: 105–118.
   Google Scholar
• Mead A, Carlton JT, Griffiths CL, Rius M. 2011. Revealing the scale of marine bioinvasions in developing regions: a South African re-assessment. Biological Invasions 13: 1991–2008.
   Web of Science ®Google Scholar
• Omori M, Hamner WM. 1982. Patchy distribution of zooplankton: behavior, population assessment and sampling problems. Marine Biology 72: 193–200
   Web of Science ®Google Scholar
• Questel JM, Hopcroft RR, DeHart HM, Smoot CA, Kosobokova KN, Bucklin A. 2021. Metabarcoding of zooplankton diversity within the Chukchi Borderland, Arctic Ocean: improved resolution from multi-gene markers and region-specific DNA databases. Marine Biodiversity 51: article 4.
   Web of Science ®Google Scholar
• Richardson AJ. 2008. In hot water: zooplankton and climate change. ICES Journal of Marine Science 65: 279–295.
   Web of Science ®Google Scholar
• Robinson TB, Alexander ME, Simon CA, Griffiths CL, Peters K, Sibanda S et al. 2016. Lost in translation? Standardizing the terminology used in marine invasion biology and updating South African alien species lists. African Journal of Marine Science 38: 129–140.
   Web of Science ®Google Scholar
• Rosenberg G. 2014. A new critical estimate of named species-level diversity of the recent Mollusca. American Malacological Bulletin 32: 308–322.
   Web of Science ®Google Scholar
• Sabatini ME, Ramírez FC, Bradford-Grieve J. 2007. Redescription of Calanoides carinatus (Krøyer) (Copepoda: Calanoida: Calanidae) with a discussion on the status of related species. Invertebrate Systematics 21: 341–364.
   Web of Science ®Google Scholar
• Shokralla S, Spall JL, Gibson JF, Hajibabaei M. 2012. Next-generation sequencing technologies for environmental DNA research. Molecular Ecology 21: 1794–1805.
   PubMed Web of Science ®Google Scholar
• Singh SP, Groeneveld JC, Al-Marzouqi A, Willows-Munro S. 2017. A molecular phylogeny of the spiny lobster Panulirus homarus highlights a separately evolving lineage from the Southwest Indian Ocean. PeerJ 5: e3356.
   PubMed Web of Science ®Google Scholar
• Singh SP, Groeneveld JC, Hart-Davis MG, Backeberg BC, Willows- Munro S. 2018. Seascape genetics of the spiny lobster Panulirus homarus in the Western Indian Ocean: understanding how oceanographic features shape the genetic structure of species with high larval dispersal potential. Ecology and Evolution 8: 12221–12237.
   PubMed Web of Science ®Google Scholar
• Steinke D, Connell AD, Hebert PDN. 2016. Linking adults and immatures of South African marine fishes. Genome 59: 959–967.
   PubMed Web of Science ®Google Scholar
• Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E. 2012. Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology 21: 2045–2050.
   PubMed Web of Science ®Google Scholar
• Turner JT. 2015. Zooplankton fecal pellets, marine snow, phytodetritus and the ocean’s biological pump. Progress in Oceanography 130: 205–248.
   Web of Science ®Google Scholar
• Vargas S, Schuster A, Sacher K, Büttner G, Schätzle S, Läuchli B et al. 2012. Barcoding sponges: an overview based on comprehensive sampling. PLoS ONE 7: e39345.
   PubMed Web of Science ®Google Scholar
• Verheye HM. 2000. Decadal-scale trends across several marine trophic levels in the southern Benguela upwelling system off South Africa. Ambio 29: 30–34.
   Web of Science ®Google Scholar
• Verheye HM, Hutchings L, Huggett JA, Painting SJ. 1992. Mesozooplankton dynamics in the Benguela ecosystem, with emphasis on the herbivorous copepods. In: Payne AIL, Brink KH, Mann KH, Hilborn R (eds), Benguela trophic functioning. South African Journal of Marine Science 12: 561–584.
   Google Scholar
• Verheye HM, Richardson AJ, Hutchings L, Marska G, Gianakouras D. 1998. Long-term trends in the abundance and community structure of coastal zooplankton in the southern Benguela system, 1951–1996. South African Journal of Marine Science 19: 317–332.
   Google Scholar
• Verheye HM, Lamont T, Huggett JA, Kreiner A, Hampton I. 2016. Plankton productivity of the Benguela Current large marine ecosystem (BCLME). Environmental Development 17: 75–92.
   Web of Science ®Google Scholar
• Ward R, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1847–1857.
   PubMed Web of Science ®Google Scholar