Inside the Archives: Molecular Ecology

DNA Barcoding

Hebert, Paul D. N., Alina Cywinska, Shelley L. Ball, and Jeremy R. deWaard. “Biological Identifications through DNA Barcodes.” Proceedings of the Royal Society of London. Series B: Biological Sciences 270, no. 1512 (February 7, 2003): 313–21. https://doi.org/10.1098/rspb.2002.2218.

Environmental DNA (eDNA) Metabarcoding

Andres, Kara J., Timothy D. Lambert, David M. Lodge, Jose Andrés, and James R. Jackson. “Combining Sampling Gear to Optimally Inventory Species Highlights the Efficiency of eDNAMetabarcoding.” Environmental DNA, October 3, 2022, edn3.366. https://doi.org/10.1002/edn3.366.

Cilleros, Kévin, Alice Valentini, Luc Allard, Tony Dejean, Roselyne Etienne, Gaël Grenouillet, Amaia Iribar, Pierre Taberlet, Régis Vigouroux, and Sébastien Brosse. “Unlocking Biodiversity and Conservation Studies in High‐diversity Environments Using Environmental DNA (EDNA): A Test with Guianese Freshwater Fishes.” Molecular Ecology Resources 19, no. 1 (January 2019): 27–46. https://doi.org/10.1111/1755-0998.12900.

Collins, Rupert A., Judith Bakker, Owen S. Wangensteen, Ana Z. Soto, Laura Corrigan, David W. Sims, Martin J. Genner, and Stefano Mariani. “Non‐specific Amplification Compromises Environmental DNA Metabarcoding with COI.” Edited by Douglas Yu. Methods in Ecology and Evolution 10, no. 11 (November 2019): 1985–2001. https://doi.org/10.1111/2041-210X.13276.

Cristescu, Melania E., and Paul D.N. Hebert. “Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation.” Annual Review of Ecology, Evolution, and Systematics 49, no. 1 (November 2, 2018): 209–30. https://doi.org/10.1146/annurev-ecolsys-110617-062306.

Laporte, M., C.S. Berger, E. García-Machado, G. Côté, O. Morissette, and L. Bernatchez. “Cage Transplant Experiment Shows Weak Transport Effect on Relative Abundance of Fish Community Composition as Revealed by EDNA Metabarcoding.” Ecological Indicators 137 (April 2022): 108785. https://doi.org/10.1016/j.ecolind.2022.108785.

Milan, David T., Izabela S. Mendes, Júnio S. Damasceno, Daniel F. Teixeira, Naiara G. Sales, and Daniel C. Carvalho. “New 12S Metabarcoding Primers for Enhanced Neotropical Freshwater Fish Biodiversity Assessment.” Scientific Reports 10, no. 1 (December 2020): 17966. https://doi.org/10.1038/s41598-020-74902-3.

Polanco F., Andrea, Eilísh Richards, Benjamin Flück, Alice Valentini, Florian Altermatt, Sébastien Brosse, Jean‐Claude Walser, et al. “Comparing the Performance of 12S Mitochondrial Primers for Fish Environmental DNA across Ecosystems.” Environmental DNA 3, no. 6 (November 2021): 1113–27. https://doi.org/10.1002/edn3.232.

Pomerantz, Aaron, Nicolás Peñafiel, Alejandro Arteaga, Lucas Bustamante, Frank Pichardo, Luis A Coloma, César L Barrio-Amorós, David Salazar-Valenzuela, and Stefan Prost. “Real-Time DNA Barcoding in a Rainforest Using Nanopore Sequencing: Opportunities for Rapid Biodiversity Assessments and Local Capacity Building.” GigaScience 7, no. 4 (April 1, 2018). https://doi.org/10.1093/gigascience/giy033.

Sales, Naiara G., Owen S. Wangensteen, Daniel C. Carvalho, and Stefano Mariani. “Influence of Preservation Methods, Sample Medium and Sampling Time on EDNA Recovery in a Neotropical River.” Environmental DNA 1, no. 2 (July 2019): edn3.14. https://doi.org/10.1002/edn3.14.

Sales, Naiara Guimarães, Owen Simon Wangensteen, Daniel Cardoso Carvalho, Kristy Deiner, Kim Præbel, Ilaria Coscia, Allan D. McDevitt, and Stefano Mariani. “Space-Time Dynamics in Monitoring Neotropical Fish Communities Using EDNA Metabarcoding.” Science of The Total Environment 754 (February 2021): 142096. https://doi.org/10.1016/j.scitotenv.2020.142096.

Spear, Michael J., Holly S. Embke, Patrick J. Krysan, and M. Jake Vander Zanden. “Application of EDNA as a Tool for Assessing Fish Population Abundance.” Environmental DNA 3, no. 1 (January 2021): 83–91. https://doi.org/10.1002/edn3.94.

Srivathsan, Amrita, Leshon Lee, Kazutaka Katoh, Emily Hartop, Sujatha Narayanan Kutty, Johnathan Wong, Darren Yeo, and Rudolf Meier. “ONTbarcoder and MinION Barcodes Aid Biodiversity Discovery and Identification by Everyone, for Everyone.” BMC Biology 19, no. 1 (December 2021): 217. https://doi.org/10.1186/s12915-021-01141-x.

Thomas, Austen C., Jesse Howard, Phong L. Nguyen, Tracie A. Seimon, and Caren S. Goldberg. “EDNA Sampler: A Fully Integrated Environmental DNA Sampling System.” Edited by Nick Golding. Methods in Ecology and Evolution 9, no. 6 (June 2018): 1379–85. https://doi.org/10.1111/2041-210X.12994.

Urban, Lara, Andre Holzer, J Jotautas Baronas, Michael B Hall, Philipp Braeuninger-Weimer, Michael J Scherm, Daniel J Kunz, et al. “Freshwater Monitoring by Nanopore Sequencing.” ELife 10 (January 19, 2021): e61504. https://doi.org/10.7554/eLife.61504.