Suggested Reading and References

Last updated on 2025-04-01 | Edit this page

Overview

Questions

  • How can I learn more?

Objectives

  • Become familiar with useful references.

Background on the Science

  1. The ecologist’s field guide to sequence‐based identification of biodiversity (Creer et al, 2016)
  2. Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA (Ruppert et al., 2019)
  3. Critical considerations for communicating environmental DNA science (Stein et al., 2024)
  4. How, What, and Where You Sample Environmental DNA Affects Diversity Estimates and Species Detection (Kirtane et al., 2024)
  5. A Guide to Environmental DNA Extractions for Non‐Molecular Trained Biologists, Ecologists, and Conservation Scientists (Rieder et al., 2024)

Data Management and Standards

  1. Publishing DNA‐derived data through biodiversity data platforms. (Finstad et al., 2023)
  2. A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics (Eloe‐Fadrosh et al., 2024)
  3. The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data. (Klymus et al. 2024)
  4. Best practices for genetic and genomic data archiving (Leigh et al., 2024)
  5. Centering accessibility, increasing capacity, and fostering innovation in the development of international eDNA standards (Hirsch et al., 2024)

Policy

  1. National Aquatic Environmental DNA Strategy (eDNA Task Team, 2024)

Standards Reference Material

  1. Publishing DNA‐derived data through biodiversity data platforms. (Finstad wt al., 2023)

Darwin Core

  1. Quick Reference Guide (term search): https://dwc.tdwg.org/terms/
  2. DNA Derived Data Extension: https://rs.gbif.org/extension/gbif/1.0/dna_derived_data_2022‐02‐23.xml

MIxS

  1. Intro: https://www.gensc.org/pages/standards‐intro.html
  2. Term search: https://genomicsstandardsconsortium.github.io/mixs/term_list/

Data Management Tools

  1. GBIF Metabarcoding Data Toolkit (MDT): https://mdt.gbif.org/
  2. MDT User Guide: https://docs.gbif‐uat.org/mdt‐user‐guide/en/
  3. GBIF‐US MDT: https://mdt.gbif.us/ ; manager: Stephen Formel (sformel@usgs.gov)
  4. NOAA Omics Data Management Guide: https://noaa‐omics‐dmg.readthedocs.io/en/latest/

Community Pages

  1. GBIF: https://www.gbif.org/dna
  2. OBIS: https://obis.org/2024/10/22/obis‐edna/

References

  • Creer, S., Deiner, K., Frey, S., Porazinska, D., Taberlet, P., Thomas, W.K., Potter, C., Bik, H.M., 2016. The ecologist’s field guide to sequence‐based identification of biodiversity. Methods in Ecology and Evolution 7, 1008–1018. https://doi.org/10.1111/2041‐210X.12574

  • eDNA Task Team of the Interagency Working Group on Biodiversity of the Subcommittee on Ocean Science and Technology Committee on Environment of the National Science & Technology Council. 2024. National Aquatic Environmental DNA Strategy. https://www.whitehouse.gov/wpcontent/uploads/2024/06/NSTC_National‐Aquatic‐eDNA‐Strategy.pdf

  • Eloe‐Fadrosh, E.A., Mungall, C.J., Miller, M.A., Smith, M., Patil, S.S., Kelliher, J.M., Johnson, L.Y.D., Rodriguez, F.E., Chain, P.S.G., Hu, B., Thornton, M.B., McCue, L.A., McHardy, A.C., Harris, N.L., Reddy, T.B.K., Mukherjee, S., Hunter, C.I., Walls, R., Schriml, L.M., 2024. A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics, in: Setubal, J.C., Stadler, P.F., Stoye, J. (Eds.), Comparative Genomics: Methods and Protocols. Springer US, New York, NY, pp. 587–609. https://doi.org/10.1007/978‐1‐0716‐3838‐5_20

  • Finstad, A.G., Andersson, A., Bissett, A., Fossøy, F., Grosjean, M., Hope, M., Kõljalg, U., Lundin, D., Nilsson, H., Prager, M., Jeppesen, T.S., Svenningsen, C., Schigel, D., Abarenkov, K., Provoost, P., Suominen, S., Frøslev, T.G., 2023. Publishing DNA‐derived data through biodiversity data platforms. https://doi.org/10.35035/DOC‐VF1A‐NR22

  • Hirsch, S., Acharya‐Patel, N., Amamoo, P.A., Borrero‐Pérez, G.H., Cahyani, N.K.D., Ginigini, J.G.M., Hurley, K.K.C., Lopes‐Lima, M., Lopez, M.L., Mapholi, N., Ouattara, K.N., Pazmiño, D.A., Rii, Y., Thompson, F., Heyden, S. von der, Watsa, M., Yepes‐Narvaez, V., Allan, E.A., Kelly, R., 2024. Centering accessibility, increasing capacity, and fostering innovation in the development of international eDNA standards. Metabarcoding and Metagenomics 8, e126058. https://doi.org/10.3897/mbmg.8.126058

  • Leigh, D.M., Vandergast, A.G., Hunter, M.E., Crandall, E.D., Funk, W.C., Garroway, C.J., Hoban, S., OylerMcCance, S.J., Rellstab, C., Segelbacher, G., Schmidt, C., Vázquez‐Domínguez, E., Paz‐Vinas, I., 2024. Best practices for genetic and genomic data archiving. Nat Ecol Evol 8, 1224–1232. https://doi.org/10.1038/s41559‐024‐02423‐7

  • Kirtane, A., Howard, L., Beaver, C.E., Hunter, M.E., Luikart, G., Deiner, K., 2024. How, What, and Where You Sample Environmental DNA Affects Diversity Estimates and Species Detection. Environmental DNA 6, e70042. https://doi.org/10.1002/edn3.70042

  • Klymus, K.E., Baker, J.D., Abbott, C.L., Brown, R.J., Craine, J.M., Gold, Z., Hunter, M.E., Johnson, M.D., Jones, D.N., Jungbluth, M.J., Jungbluth, S.P., Lor, Y., Maloy, A.P., Merkes, C.M., Noble, R., Patin, N.V., Sepulveda, A.J., Spear, S.F., Steele, J.A., Takahashi, M., Watts, A.W., Theroux, S., 2024. The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data. Metabarcoding and Metagenomics 8, e128689. https://doi.org/10.3897/mbmg.8.128689

  • Rieder, J., Jemmi, E., Hunter, M.E., Adrian‐Kalchhauser, I., 2024. A Guide to Environmental DNA Extractions for Non‐Molecular Trained Biologists, Ecologists, and Conservation Scientists. Environmental DNA 6, e70002. https://doi.org/10.1002/edn3.70002

  • Ruppert, K.M., Kline, R.J., Rahman, M.S., 2019. Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Global Ecology and Conservation 17, e00547. https://doi.org/10.1016/j.gecco.2019.e00547

  • Stein, E.D., Jerde, C.L., Allan, E.A., Sepulveda, A.J., Abbott, C.L., Baerwald, M.R., Darling, J., Goodwin, K.D., Meyer, R.S., Timmers, M.A., Thielen, P.M., 2024. Critical considerations for communicating environmental DNA science. Environmental DNA 6, e472. https://doi.org/10.1002/edn3.472