A DNA Barcode Dataset for the Aquatic Fauna of the Panama Canal: Novel Resources for Detecting Faunal Change in the Neotropics
Abstract
1. Summary
2. Data Description
3. Methods
4. Scientific Relevance and Considerations
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
STRI | Smithsonian Tropical Research Institute |
ACP | Autoridad del Canal de Panamá (Panama Canal Authority) |
COI | Cytochrome c oxidase subunit I |
DNA | Deoxyribonucleic acid |
PCR | Polymerase Chain Reaction |
References
- Taberlet, P.; Coissac, E.; Pompanon, F.; Brochmann, C.; Willeslev, E. Towards next-generation biodiversity assessment using DNA metabarcoding. Mol. Ecol. 2012, 21, 2045–2050. [Google Scholar] [CrossRef] [PubMed]
- Zhang, S.; Zhao, J.; Yao, M. A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish. Methods Ecol. Evol. 2020, 11, 1609–1625. [Google Scholar] [CrossRef]
- Schreiber, L.; Castellanos-Galindo, G.A.; Robertson, D.R.; Torchin, M.; Chavarria, K.; Laakmann, S.; Saltonstall, K. Environmental DNA (eDNA) reveals potential for interoceanic fish invasions across the Panama Canal. Ecol. Evol. 2023, 13, e9675. [Google Scholar] [CrossRef]
- Collins, R.A.; Bakker, J.; Wangensteen, O.S.; Soto, A.Z.; Corrigan, L.; Sims, D.W.; Genner, M.J.; Mariani, S. Non-specific amplification compromises environmental DNA metabarcoding with COI. Methods Ecol. Evol. 2019, 10, 1985–2001. [Google Scholar] [CrossRef]
- Andres, K.J.; Lodge, D.M.; Sethi, S.A.; Andrés, J. Detecting and analysing intraspecific genetic variation with eDNA: From population genetics to species abundance. Mol. Ecol. 2023, 32, 4118–4132. [Google Scholar] [CrossRef]
- Rodgers, T.W.; Xu, C.C.Y.; Giacalone, J.; Kapheim, K.M.; Saltonstall, K.; Vargas, M.; Yu, D.W.; Somervuo, P.; McMillan, W.O.; Jansen, P.A. Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: Evidence from a known tropical mammal community. Mol. Ecol. Resour. 2017, 17, e133–e145. [Google Scholar] [CrossRef]
- Casey, J.M.; Meyer, C.P.; Morat, F.; Brandl, S.J.; Planes, S.; Parravicini, V. Reconstructing hyperdiverse food webs: Gut content metabarcoding as a tool to disentangle trophic interactions on coral reefs. Methods Ecol. Evol. 2019, 10, 1157–1170. [Google Scholar] [CrossRef]
- Hildebrand, S.F. The Panama Canal as a passageway for fishes, with lists and remarks on the fishes and invertebrates observed. Zoologica 1938, 24, 15–45. [Google Scholar] [CrossRef]
- Rubinoff, R.W.; Rubinoff, I.R.A. Interoceanic Colonization of a Marine Goby through the Panama Canal. Nature 1968, 217, 476–478. [Google Scholar] [CrossRef]
- Zaret, T.M.; Paine, R.T. Species Introduction in a Tropical Lake: A newly introduced piscivore can produce population changes in a wide range of trophic levels. Science 1973, 182, 449–455. [Google Scholar] [CrossRef]
- McCosker, J.E.; Dawson, C.E. Biotic Passage through the Panama Canal, with Particular Reference to Fishes. Mar. Biol. 1975, 30, 343–351. [Google Scholar] [CrossRef]
- Gunter, G. Marine Fishes of Panama as Related to the Canal. Gulf Res. Rep. 1979, 6, 267–273. [Google Scholar] [CrossRef]
- Angehr, G. Rapid Long-distance Colonization of Lake Gatun, Panama, by Snail Kites. Wilson Bull. 1999, 11, 265–268. [Google Scholar]
- Smith, S.A.; Bell, G.; Bermingham, E. Cross–Cordillera exchange mediated by the Panama Canal increased the species richness of local freshwater fish assemblages. Proc. R. Soc. London. Ser. B Biol. Sci. 2004, 271, 1889–1896. [Google Scholar] [CrossRef] [PubMed]
- Sharpe, D.M.T.; De León, L.F.; González, R.; Torchin, M.E. Tropical fish community does not recover 45 years after predator introduction. Ecology 2017, 98, 412–424. [Google Scholar] [CrossRef]
- Guzman, H.M.; Real, C.K. Have Antillean manatees (Trichechus manatus manatus) entered the Eastern Pacific Ocean? Mar. Mammal Sci. 2023, 39, 274–280. [Google Scholar] [CrossRef]
- Castrellón, M.G.; Lu, C.; Domínguez, I.; Matos, R.; Anguizola, K.; Popescu, I. Spatiotemporal distribution of salinity in Gatun Lake and the Panama Canal pre- and post-expansion. J. Hydrol. Reg. Stud. 2025, 58, 102199. [Google Scholar] [CrossRef]
- Castellanos-Galindo, G.A.; Robertson, D.R.; Sharpe, D.M.T.; Torchin, M.E. A new wave of marine fish invasions through the Panama and Suez canals. Nat. Ecol. Evol. 2020, 4, 1444–1446. [Google Scholar] [CrossRef]
- Folmer, O.; Black, M.; Hoeh, W.; Lutz, R.; Vrijenhoek, R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 1994, 3, 294–299. [Google Scholar]
- Hebert, P.D.N.; Cywinska, A.; Ball, S.L.; deWaard, J.R. Biological identifications through DNA barcodes. Proc. R. Soc. B Biol. Sci. 2003, 270, 313–321. [Google Scholar] [CrossRef]
- Ratnasingham, S.; Hebert, P.D. BOLD: The Barcode of Life Data System (http://www.barcodinglife.org). Mol. Ecol. Notes 2007, 7, 355–364. [Google Scholar] [CrossRef]
- Marceniuk, A.P.; Caires, R.A.; Rotundo, M.M.; Cerqueira, N.; Siccha-Ramirez, R.; Wosiacki, W.B.; Oliveira, C. Taxonomic revision of the Menticirrhus americanus (Linnaeus, 1758) and M. littoralis (Holbrook, 1847) (Percomorphacea: Sciaenidae) species complexes from the western Atlantic. Zootaxa 2020, 4822, 301–333. [Google Scholar] [CrossRef] [PubMed]
- Torres-Hernández, E.; Betancourt-Resendes, I.; Angulo, A.; Robertson, D.R.; Barraza, E.; Espinoza, E.; Díaz-Jaimes, P.; Domínguez-Domínguez, O. A multi-locus approach to elucidating the evolutionary history of the clingfish Tomicodon petersii (Gobiesocidae) in the Tropical Eastern Pacific. Mol. Phylogenetics Evol. 2022, 166, 107316. [Google Scholar] [CrossRef] [PubMed]
- URS Holdings, Inc. Panama Canal Expansion Project—Third Set of Locks: Category III Environmental Impact Study; URS Holdings, Inc.: San Francisco, CA, USA, 2007. [Google Scholar]
- Zietara, M.S.; Arndt, A.; Geets, A.; Hellemans, B.; Volckaert, F.A. The nuclear rDNA region of Gyrodactylus arcuatus and G. branchicus (Monogenea: Gyrodactylidae). J. Parasitol. 2000, 86, 1368–1373. [Google Scholar] [CrossRef]
- Palumbi, S.; Martin, A.; Romano, S.; McMillan, W.O.; Stice, L.; Grabowski, G. The Simple Fool’s Guide to PCR; University of Hawaii: Honolulu, HI, USA, 2002. [Google Scholar]
- Li, C.; Ortí, G. Molecular phylogeny of Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences. Mol. Phylogenetics Evol. 2007, 44, 386–398. [Google Scholar] [CrossRef]
- Baldwin, C.C.; Mounts, J.H.; Smith, D.G.; Weigt, L.A. Genetic identification and color descriptions of early life-history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with Comments on identification of adult Phaeoptyx. Zootaxa 2009, 2008, 1–22. [Google Scholar] [CrossRef]
- Hebert, P.D.N.; Stoeckle, M.Y.; Zemlak, T.S.; Francis, C.M. Identification of Birds through DNA Barcodes. PLoS Biol. 2004, 2, e312. [Google Scholar] [CrossRef]
- Tavares, E.S.; Baker, A.J. Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds. BMC Evol. Biol. 2008, 8, 81. [Google Scholar] [CrossRef] [PubMed]
- Coeur d’acier, A.; Cruaud, A.; Artige, E.; Genson, G.; Clamens, A.-L.; Pierre, E.; Hudaverdian, S.; Simon, J.-C.; Jousselin, E.; Rasplus, J.-Y. DNA Barcoding and the Associated PhylAphidB@se Website for the Identification of European Aphids (Insecta: Hemiptera: Aphididae). PLoS ONE 2014, 9, e97620. [Google Scholar] [CrossRef]
- Meyer, C.P. Molecular systematics of cowries (Gastropoda: Cypraeidae) and diversification patterns in the tropics. Biol. J. Linn. Soc. 2003, 79, 401–459. [Google Scholar] [CrossRef]
- Bowles, J.; McManus, D.P. Rapid discrimination of Echinococcus species and strains using a polymerase chain reaction-based RFLP method. Mol. Biochem. Parasitol. 1993, 57, 231–239. [Google Scholar] [CrossRef] [PubMed]
- Miura, O.; Kuris, A.M.; Torchin, M.E.; Hechinger, R.F.; Dunham, E.J.; Chiba, S. Molecular-genetic analyses reveal cryptic species of trematodes in the intertidal gastropod, Batillaria cumingi (Crosse). Int. J. Parasitol. 2005, 35, 793–801. [Google Scholar] [CrossRef] [PubMed]
Locus | |||||
---|---|---|---|---|---|
Phylum | Class | Order | COI | 12S | 16S |
Arthropoda | Arachnida | Trombidiformes | 3 | 0 | 0 |
Branchiopoda | Anomopoda | 23 | 0 | 0 | |
Ctenopoda | 4 | 0 | 0 | ||
Copepoda | Calanoida | 2 | 0 | 0 | |
Cyclopoida | 23 | 0 | 0 | ||
Insecta | Coleoptera | 8 | 0 | 0 | |
Diptera | 21 | 0 | 0 | ||
Ephemeroptera | 38 | 0 | 0 | ||
Hemiptera | 54 | 0 | 0 | ||
Lepidoptera | 1 | 0 | 0 | ||
Megaloptera | 5 | 0 | 0 | ||
Neuroptera | 6 | 0 | 0 | ||
Odonata | 47 | 0 | 0 | ||
Plecoptera | 7 | 0 | 0 | ||
Trichoptera | 18 | 0 | 0 | ||
Unknown | 1 | 0 | 0 | ||
Malacostraca | Amphipoda | 1 | 0 | 0 | |
Decapoda | 64 | 0 | 36 | ||
Ostracoda Unknown | 14 | 0 | 0 | ||
6 | 0 | 0 | |||
Chordata | Actinopterygii | Acanthuriformes | 5 | 6 | 6 |
Atheriniformes | 3 | 2 | 2 | ||
Beloniformes | 6 | 4 | 4 | ||
Blenniiformes | 1 | 0 | 0 | ||
Carangiformes | 98 | 47 | 63 | ||
Characiformes | 31 | 14 | 12 | ||
Cichliformes | 18 | 6 | 7 | ||
Clupeiformes | 5 | 3 | 3 | ||
Cyprinodontiformes | 27 | 4 | 42 | ||
Elopiformes | 7 | 4 | 7 | ||
Gobiiformes | 30 | 11 | 13 | ||
Gymnotiformes | 1 | 0 | 0 | ||
Holocentriformes | 0 | 0 | 1 | ||
Mugiliformes | 4 | 2 | 2 | ||
Perciformes | 61 | 42 | 39 | ||
Siluriformes | 28 | 4 | 3 | ||
Spariformes | 1 | 1 | 1 | ||
Synbranchiformes | 3 | 1 | 1 | ||
Syngnathiformes | 2 | 0 | 1 | ||
Chondrichthyes | Carcharhiniformes | 1 | 0 | 0 | |
Aves | Anseriformes | 3 | 0 | 0 | |
Charadriiformes | 36 | 0 | 0 | ||
Coraciiformes | 4 | 0 | 0 | ||
Gruiformes | 2 | 0 | 0 | ||
Pelecaniformes | 5 | 0 | 0 | ||
Mammalia | Sirenia | 2 | 0 | 0 | |
Reptilia | Crocodilia | 5 | 0 | 0 | |
Squamata | 2 | 0 | 2 | ||
Testudines | 5 | 0 | 7 | ||
Cnidaria | Hydrozoa | Anthoathecata | 4 | 0 | 0 |
Mollusca | Bivalvia | Mytilidae | 1 | 0 | 0 |
Unionida | 2 | 0 | 0 | ||
Venerida | 2 | 0 | 0 | ||
Gastropoda | Architaenioglossa | 3 | 0 | 0 | |
Cerithiodea | 1 | 0 | 0 | ||
Lymnaeoidea | 1 | 0 | 0 | ||
Platyhelminthes | Trematoda | Opisthorchiida | 3 | 0 | 0 |
Plagiorchiida | 1 | 0 | 0 | ||
Unknown | 1 | 0 | 0 | ||
Rotifera | Bdelloidea | Philodinida | 1 | 0 | 0 |
Ploima | 36 | 0 | 0 |
Locus | Taxonomic Groups | Forward Primer | Reverse Primer | Source |
---|---|---|---|---|
COI | Fishes | FISH-BCL: TCAACYAATCAYAAAGATATYGGCAC | FISH-BCH: ACTTCYGGGTGRCCRAARAATCA | [28] |
Birds | BirdF1: TTCTCCAACCACAAAGACATTGGCAC Ltyr: TGTAAAAAGGWCTACAGCCTAACGC | BirdR1: ACGTGGGAGATAATTCCAAATCCTG COI907aH2: GTRGCNGAYGTRAARTATGCTCG | [29,30] | |
Reptiles Mammals | FISH-BCL: TCAACYAATCAYAAAGATATYGGCAC LCO1490: GGTCAACAAATCATAAAGATATTGG | FISH-BCH: ACTTCYGGGTGRCCRAARAATCA HCO2198: TAAACTTCAGGGTGACAAAAAATCA | [19,28] | |
Arthropods * Crustacea Mollusks | LCO1490: GGTCAACAAATCATAAAGATATTGG dgLCO1490: GGTCAACAAATCATAAAGAYATYGG | HCO2198: TAAACTTCAGGGTGACAAAAAATCA dgHCO2198: TAAACTTCAGGGTGACCAAARAAYCA HCO2198puc: TAAACTTCWGGRTGWCCAAARAATC | [19,31,32] | |
Trematodes | JB3: TTTTTTGGGCATCCTGAGGTTTAT | COI-Rtrema: CAACAAATCATGATGCAAAAGG | [33,34] | |
12S | Fishes | 12S229F: GYCGGTAAAAYTCGTGCCAG | 12S954R: YCCAAGYGCACCTTCCGGTA | [27] |
16S | Fishes Crustacea | 16Sar: CGCCTGTTTATCAAAAACAT | 16Sbr: CCGGTCTGAACTCAGATCACGT | [26] |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Saltonstall, K.; Collin, R.; Aguilar, C.; Alda, F.; Baldrich-Mora, L.M.; Bravo, V.; Castillo, M.F.; Castro, S.; De León, L.F.; Díaz-Ferguson, E.; et al. A DNA Barcode Dataset for the Aquatic Fauna of the Panama Canal: Novel Resources for Detecting Faunal Change in the Neotropics. Data 2025, 10, 108. https://doi.org/10.3390/data10070108
Saltonstall K, Collin R, Aguilar C, Alda F, Baldrich-Mora LM, Bravo V, Castillo MF, Castro S, De León LF, Díaz-Ferguson E, et al. A DNA Barcode Dataset for the Aquatic Fauna of the Panama Canal: Novel Resources for Detecting Faunal Change in the Neotropics. Data. 2025; 10(7):108. https://doi.org/10.3390/data10070108
Chicago/Turabian StyleSaltonstall, Kristin, Rachel Collin, Celestino Aguilar, Fernando Alda, Laura M. Baldrich-Mora, Victor Bravo, María Fernanda Castillo, Sheril Castro, Luis F. De León, Edgardo Díaz-Ferguson, and et al. 2025. "A DNA Barcode Dataset for the Aquatic Fauna of the Panama Canal: Novel Resources for Detecting Faunal Change in the Neotropics" Data 10, no. 7: 108. https://doi.org/10.3390/data10070108
APA StyleSaltonstall, K., Collin, R., Aguilar, C., Alda, F., Baldrich-Mora, L. M., Bravo, V., Castillo, M. F., Castro, S., De León, L. F., Díaz-Ferguson, E., Garcés, H. A., Gómez, E., González, R. G., González-Torres, M. A., Guzman, H. M., Hiller, A., Ibáñez, R., Jaramillo, C., Kaiser, K. L., ... Castellanos-Galindo, G. (2025). A DNA Barcode Dataset for the Aquatic Fauna of the Panama Canal: Novel Resources for Detecting Faunal Change in the Neotropics. Data, 10(7), 108. https://doi.org/10.3390/data10070108