journal article Open Access Jul 06, 2021

Aquatic Organisms Research with DNA Barcodes

Diversity Vol. 13 No. 7 pp. 306 · MDPI AG
View at Publisher Save 10.3390/d13070306
Abstract
Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.
Topics

No keywords indexed for this article. Browse by subject →

References
171
[1]
Biological identifications through DNA barcodes

Paul D. N. Hebert, Alina Cywinska, Shelley L. Ball et al.

Proceedings of the Royal Society of London. Series... 2003 10.1098/rspb.2002.2218
[2]
Hubert, N., Hanner, R., Holm, E., Mandrak, N.E., Taylor, E., Burridge, M., Watkinson, D., Dumont, P., Curry, A., and Bentzen, P. (2008). Identifying Canadian Freshwater Fishes through DNA Barcodes. PLoS ONE, 3. 10.1371/journal.pone.0002490
[3]
Comprehensive DNA barcode coverage of North American birds

KEVIN C. R. KERR, Mark Y. Stoeckle, CARLA J. DOVE et al.

Molecular Ecology Notes 2007 10.1111/j.1471-8286.2007.01670.x
[4]
A DNA ‘Barcode Blitz’: Rapid Digitization and Sequencing of a Natural History Collection

Paul D. N. Hebert, Jeremy R. deWaard, Evgeny V. Zakharov et al.

PLoS ONE 10.1371/journal.pone.0068535
[5]
Schmidt "DNA Barcoding Largely Supports 250 Years of Classical Taxonomy: Identifications for Central European Bees (Hymenoptera, Apoidea Partim)" Mol. Ecol. Resour. (2015) 10.1111/1755-0998.12363
[6]
Monaghan "Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation" Syst. Biol. (2009) 10.1093/sysbio/syp027
[7]
A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System

Sujeevan Ratnasingham, Paul D. N. Hebert

PLoS ONE 10.1371/journal.pone.0066213
[8]
Kekkonen "DNA Barcode-Based Delineation of Putative Species: Efficient Start for Taxonomic Workflows" Mol. Ecol. Resour. (2014) 10.1111/1755-0998.12233
[9]
Hebert "Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator" Proc. Natl. Acad. Sci. USA (2004) 10.1073/pnas.0406166101
[10]
Smith "Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections" Proc. Natl. Acad. Sci. USA (2008) 10.1073/pnas.0805319105
[11]
Ratnasingham "Bold: The Barcode of Life Data System (www.Barcodinglife.Org)" Mol. Ecol. Notes (2007) 10.1111/j.1471-8286.2007.01678.x
[12]
Bucklin "Barcoding of Marine Metazoa" Annu. Rev. Mar. Sci. (2011) 10.1146/annurev-marine-120308-080950
[13]
Trivedi "Role of DNA barcoding in marine biodiversity assessment and conservation: An update" Saudi J. Biol. Sci. (2016) 10.1016/j.sjbs.2015.01.001
[14]
Mauchline, J., Blaxter, J.H.S., Southward, A.J., and Tyler, P.A. (1998). The Biology of Calanoid Copepods—Introduction. Advances in Marine Biology, Academic Press. Reprint, Not in File.
[15]
Bucklin "“Rosetta Stone” for metazoan zooplankton: DNA barcode analysis of species diversity of the Sargasso Sea (Northwest Atlantic Ocean)" Deep Sea Res. Part II Top. Stud. Oceanogr. (2010) 10.1016/j.dsr2.2010.09.025
[16]
Evaluation of ITS2-28S as a molecular marker for identification of calanoid copepods in the subtropical western North Pacific

Junya Hirai, Shinji Shimode, Atsushi Tsuda

Journal of Plankton Research 2013 10.1093/plankt/fbt016
[17]
Karanovic "Shell and Appendages Variability in Two Allopatric Ostracod Species Seen through the Light of Molecular Data" Contrib. Zool. (2020) 10.1163/18759866-20191423
[18]
Jeffery, N.W., Elías-Gutiérrez, M., and Adamowicz, S.J. (2011). Species Diversity and Phylogeographical Affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada. PLoS ONE, 6. 10.1371/journal.pone.0018364
[19]
Rowe "Three new cryptic species of the freshwater zooplankton genus Holopedium (Crustacea: Branchiopoda: Ctenopoda), revealed by genetic methods" Zootaxa (2007) 10.11646/zootaxa.1656.1.1
[20]
Improved protocols to accelerate the assembly of DNA barcode reference libraries for freshwater zooplankton

Manuel Elías‐Gutiérrez, Martha Valdez‐Moreno, Janet Topan et al.

Ecology and Evolution 2018 10.1002/ece3.3742
[21]
Wattier "Continental-scale patterns of hyper-cryptic diversity within the freshwater model taxon Gammarus fossarum (Crustacea, Amphipoda)" Sci. Rep. (2020) 10.1038/s41598-020-73739-0
[22]
Galimberti "Italian Odonates in the Pandora’s Box: A Comprehensive DNA Barcoding Inventory Shows Taxonomic Warnings at the Holarctic Scale" Mol. Ecol. Resour. (2021) 10.1111/1755-0998.13235
[23]
Denys "Morphological and Molecular Evidence of Three Species of Pikes Esox spp. (Actinopterygii, Esocidae) in France, Including the Description of a New Species" C. R. Biol. (2014) 10.1016/j.crvi.2014.07.002
[24]
Denys "Revision of Phoxinus in France with the Description of Two New Species (Teleostei, Leuciscidae)" Cybium (2020)
[25]
Buj "Cryptic diversity in Telestes pleurobipunctatus (Actinopterygii; Leuciscidae) as a consequence of historical biogeography in the Ionian Freshwater Ecoregion (Greece, Albania)" Hydrobiology (2019) 10.1007/s10750-019-3935-6
[26]
Epitashvili "Towards retrieving the Promethean treasure: A first molecular assessment of the freshwater fish diversity of Georgia" Biodivers. Data J. (2020) 10.3897/bdj.8.e57862
[27]
Ivanova "Using DNA barcodes to connect adults and early life stages of marine fishes from the Yucatan Peninsula, Mexico: Potential in fisheries management" Mar. Freshw. Res. (2010) 10.1071/mf09222
[28]
Valdez-Moreno, M., Ivanova, N.V., Elías-Gutiérrez, M., Contreras-Balderas, S., and Hebert, P.D.N. (2007). DNA Barcodes in Freshwater Fishes from Mexico and Guatemala. J. Fish Biol., submitted.
[29]
Carrillo "Identifying pelagic fish eggs in the southeast Yucatan Peninsula using DNA barcodes" Genome (2016) 10.1139/gen-2015-0151
[30]
Carrillo "First larval record of Pterois volitans (Pisces: Scorpaenidae) collected from the ichthyoplankton in the Atlantic" Biol. Invasions (2011) 10.1007/s10530-011-9968-z
[31]
Victor "The larval, juvenile, and adult stages of the Caribbean goby, Coryphopterus kuna (Teleostei: Gobiidae): A reef fish with a pelagic larval duration longer than the post-settlement lifespan" Zootaxa (2010) 10.11646/zootaxa.2346.1.5
[32]
Victor "Hypoplectrus floridae n. sp. and Hypoplectrus ecosur n. sp., Two New Barred Hamlets from the Gulf of Mexico (Pisces: Serranidae): More Than 3% Different in COI MtDNA Sequence from the Caribbean Hypoplectrus Species Flock" J. Ocean Sci. Found. (2012)
[33]
Ahern "DNA sequencing of fish eggs and larvae reveals high species diversity and seasonal changes in spawning activity in the southeastern Gulf of California" Mar. Ecol. Prog. Ser. (2018) 10.3354/meps12446
[34]
Bearez "Polylepion russelli (Labridae), a Trans-Indo-Pacific Species" Cybium (2013)
[35]
Victor "Rediscovery of Sagittalarva inornata n. gen., n. comb. (Gilbert, 1890) (Perciformes: Labridae), a long-lost deepwater fish from the eastern Pacific Ocean: A case study of a forensic approach to taxonomy using DNA barcoding" Zootaxa (2013) 10.11646/zootaxa.3669.4.8
[36]
"DNA barcoding of the ichthyofauna of Pánuco–Tamesí complex: Evidence for taxonomic conflicts in some groups" Mitochondrial DNA (2012) 10.3109/19401736.2012.710207
[37]
Venegas, R.D.L.P., Hueter, R., Cano, J.G., Tyminski, J., Remolina, J.G., Maslanka, M., Ormos, A., Weigt, L., Carlson, B., and Dove, A. (2011). An Unprecedented Aggregation of Whale Sharks, Rhincodon typus, in Mexican Coastal Waters of the Caribbean Sea. PLoS ONE, 6. 10.1371/journal.pone.0018994
[38]
Nogueira "Overlooked biodiversity of mitochondrial lineages in Hemiodus (Ostariophysi, Characiformes)" Zool. Scr. (2021) 10.1111/zsc.12469
[39]
Spier "Plectorhinchus macrolepis (Actinopterygii: Haemulidae) in the western Atlantic Ocean" J. Fish Biol. (2019) 10.1111/jfb.14117
[40]
Arruda, P.S.S., Ferreira, D.C., Oliveira, C., and Venere, P.C. (2019). DNA Barcoding Reveals High Levels of Divergence among Mitochondrial Lineages of Brycon (Characiformes, Bryconidae). Genes, 10. 10.3390/genes10090639
[41]
Caires "The Tonkin Weakfish, Cynoscion similis (Sciaenidae, Perciformes), an Endemic Species of the Amazonas-Orinoco Plume" Acta Amaz. (2019) 10.1590/1809-4392201803481
[42]
Carvalho "Integrative Taxonomy of the Species Complex Haemulon steindachneri (Jordan and Gilbert, 1882) (Eupercaria; Haemulidae) with a Description of a New Species from the Western Atlantic" Zoology (2020) 10.1016/j.zool.2020.125782
[43]
Cardoso "Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus" Mol. Phylogenetics Evol. (2020) 10.1016/j.ympev.2019.106711
[44]
Ferrette "DNA-based species identification of shark finning seizures in Southwest Atlantic: Implications for wildlife trade surveillance and law enforcement" Biodivers. Conserv. (2019) 10.1007/s10531-019-01862-0
[45]
Mateussi "Molecular Delimitation and Taxonomic Revision of the Wimple Piranhacatoprion (Characiformes: Serrasalmidae) with the Description of a New Species" J. Fish Biol. (2020) 10.1111/jfb.14417
[46]
Mattox "A New Miniature Species of Priocharax (Teleostei: Characiformes: Characidae) from the Rio Madeira Drainage, Brazil, with Comments on the Adipose Fin in Characiforms" Vertebr. Zool. (2020)
[47]
Hashimoto "A molecular assessment of species diversity in Tympanopleura and Ageneiosus catfishes (Auchenipteridae: Siluriformes)" J. Fish Biol. (2020) 10.1111/jfb.14173
[48]
Pereira "DNA barcoding reveals hidden diversity in the Neotropical freshwater fish Piabina argentea (Characiformes: Characidae) from the Upper Paraná Basin of Brazil" Mitochondrial DNA (2011) 10.3109/19401736.2011.588213
[49]
Castro Paz, F.P., Batista, J.D., and Porto, J.I.R. (2014). DNA Barcodes of Rosy Tetras and Allied Species (Characiformes: Characidae: Hyphessobrycon) from the Brazilian Amazon Basin. PLoS ONE, 9. 10.1371/journal.pone.0098603
[50]
Benzaquem, D.C., Oliveira, C., Batista, J.D.S., Zuanon, J., and Porto, J.I.R. (2015). DNA Barcoding in Pencilfishes (Lebiasinidae: Nannostomus) Reveals Cryptic Diversity across the Brazilian Amazon. PLoS ONE, 10. 10.1371/journal.pone.0112217

Showing 50 of 171 references

Cited By
18
Relevance of DNA barcodes for biomonitoring of freshwater animals

Manuel Elias-Gutierrez, Martha Valdez-Moreno · 2023

Frontiers in Environmental Science
Related

You May Also Like