Talk:Environmental DNA

Adding sources

Hello all-- Here are the following papers I'll be using as my key references. Comments? Advice?

• Biggs et al., Using eDNA to develop a national citizen science-based monitoring program for the great crested newt (Triturus cristatus), 2015, "Biological Conservation"
• Bohmann et al., Environmental DNA for wildlife biology and biodiversity monitoring, 2014, "Trends in Ecology and Evolution"
• Goldberg et al., Moving environmental DNA methods from concept to practice for monitoring aquatic macroorganisms, 2015, "Biological Conservation"
• Thomsen and Willerslev, Environmental DNA-An emerging tool in conservation for monitoring past and present biodiversity, 2015, "Biological Conservation"

Leahc 10 (talk) 04:21, 3 February 2017 (UTC)

Suggested updates

1. Provide clearer definition of eDNA and what it does/does not include
2. Brief history of discovery
3. Include application to monitoring biodiversity, species distribution, population dynamics, etc. The focus of each of these can be further broken down into different macro- and micro-environments (surface soil, various types of sediment, bodies of water)
4. Include summary of techniques for eDNA sample collection/sequencing/analysis and, of course, the challenges presented with these approaches
5. Controversial perspectives of application of eDNA to differ disciplines of biology including but not limited to molecular biology, ecology, paleontology, conservation genetics, and geology.
6. Needs additional support/citations. Possible bias from 2nd listed reference.

Leahc 10 (talk) 19:22, 25 January 2017 (UTC)

Advanced Genetics 3595 at UWO

I am going to be editing this article over the next 2 months for my Advanced Genetics class at Western University. Any suggestions would be greatly appreciated! Asincl29 (talk) 16:26, 16 October 2015 (UTC)

Changes to "Collection: Aquatic (water column)"

My proposed changes to this segment of the Wikipedia page reflect the changing nature of current environmental DNA research. The majority of eDNA work is being conducted with water collected from the water column, and the information available in the associated section of the Wikipedia page should reflect changes to this section of eDNA research and the more advanced methodology concerning that work.

See below for the proposed changes. In brackets are material already published on the page.

<The use of eDNA in aquatic sediment has been useful, but can even be applied to open water for present day study. Before eDNA, the main ways to study open water diversity was to use fishing and trapping, which requires funding and skilled labor, and other various resources, but eDNA only needs samples of water.> The majority of recent environmental DNA studies focus on samples taken from the water column [1][2]. Recent studies have included tests with fishes, amphibians, aquatic mammals, and other organisms [2]. More data is needed to determine the ability of environmental DNA samples to estimate population sizes [3]. Currently, many studies use presence/absence data as the response variable from environmental DNA tests. A volume of water (averaging ~2 L per sample) is filtered through a filter paper by use of a hand pump or peristaltic pump, and samples are stored for later laboratory analysis [4][5]. Samples filtered from water samples can be stored by freezing the samples or desiccating them in ethanol [6]. <This method is effective as pH of the water does not affect the DNA as much as previously thought, and can be made more sensitive with relative ease. Sensitivity is how likely the DNA marker will be present in the sampled water, and can be increased simply by taking more samples, having bigger samples, and increasing PCR. eDNA degrades relatively fast in the water column, which is very beneficial in short term conservation studies such as identifying what species are present.> [1] Jerde, C.L., Mahon, A.R., Chadderton, W.L. and Lodge, D.M., 2011. “Sight‐unseen” detection of rare aquatic species using environmental DNA. Conservation Letters, 4(2), pp.150-157. [2] Thomsen, P.F. and Willerslev, E., 2015. Environmental DNA–An emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation, 183, pp.4-18. [3] Evans, N.T., Olds, B.P., Renshaw, M.A., Turner, C.R., Li, Y., Jerde, C.L., Mahon, A.R., Pfrender, M.E., Lamberti, G.A. and Lodge, D.M., 2016. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Molecular Ecology Resources, 16(1), pp.29-41. [4] Rees, H.C., Maddison, B.C., Middleditch, D.J., Patmore, J.R. and Gough, K.C., 2014. The detection of aquatic animal species using environmental DNA–a review of eDNA as a survey tool in ecology. Journal of Applied Ecology, 51(5), pp.1450-1459. [5] Pilliod, D.S., Goldberg, C.S., Arkle, R.S. and Waits, L.P., 2013. Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples. Canadian Journal of Fisheries and Aquatic Sciences, 70(8), pp.1123-1130. [6] Renshaw, M.A., Olds, B.P., Jerde, C.L., McVeigh, M.M. and Lodge, D.M., 2015. The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol–chloroform–isoamyl alcohol DNA extraction. Molecular ecology resources, 15(1), pp.168-176. — Preceding unsigned comment added by AlexWiebe1 (talk • contribs) 13:48, 9 November 2017 (UTC)

GA Review

This review is transcluded from Talk:Environmental DNA/GA1. The edit link for this section can be used to add comments to the review.

Reviewer: Jens Lallensack (talk · contribs) 19:45, 2 January 2022 (UTC)

Few comments for a start, more later:

• The lead should not have inline citations (because all info + references need to be repeated in the body in any case); removing them may also look less cluttered.
• Some images appear very big compared to most other articles. I find it a bit problematic that under the section "Aquatic (water column)", three large images come together making it very cluttered with a lot of white space.
• "Environmental RNA", empty heading? If this is a sub-topic of "Environmental DNA", then we need a summary of the most important information in this section. If it is not a sub-topic, but a sister topic, I think this section needs to be removed ("Sea also" would be a better place for it in that case).
• Having inline citations in brackets "([27])" seems sub-standard and inconsistent.
• I didn't read yet, but the article structure confuses me. Having an overview section is great. But for example, the sub-sections in "Monitoring species" appear quite random to me. Each sub-section seems to be highly specialised on a specific field (e.g., fisheries) when I would expect a general overview. And having "DNA from the air" under "Mammals" does not make sense to me; why should't it work on birds, for example? The title of the paper is: "Proof of concept that animal DNA can be collected from air sampling" – that they happen to use mammals seems not to be that relevant. --Jens Lallensack (talk) 19:45, 2 January 2022 (UTC)
• Lead: eDNA metabarcoding is a novel method – this doesn't really connect with the previous paragraph, and I found it difficult to follow. Better introduce "eDNA metabarcoding" for extra clarity?
• Relating to above comment: known as metagenomics, metabarcoding, and single-species detection – As a reader, I am at a loss here; in the next paragraph, only metabarcoding is discussed, not metagenomics, and metabarcoding is linked twice but to separate articles, and the reader does not know why.
• a novel method – we should avoid words such as "novel", because that would be outdated in a few years. When important, give the approximate date.
• This method allows for biomonitoring without requiring collection of the living organism, creating the ability to study organisms that are invasive, elusive, or endangered without introducing anthropogenic stress on the organism. – Why shouldn't we introduce anthropogenic stress on an invasive species? That argument only seems to be valid for the endangered species? Or, asked the other way around: Why restrict to "invasive, elusive, or endangered" species? Instead I thought that assessment of overall biodiversity is one of the main goals?
• The analysis of eDNA has great potential, not only for monitoring common species, but to genetically detect and identify other extant species that could influence conservation efforts. – So that means we mostly monitor common species with this method? This seems to be a small part of the picture only?
• Importantly, eDNA is often more cost-effective compared to traditional sampling methods. – If we can avoid "importantly", we should, and this is a case where we easily can. I don't think it adds anything.
• applied in many subenvironments such as freshwater sampling, seawater sampling – both are listed as "macro environments" in the previous sentence. --Jens Lallensack (talk) 20:05, 2 January 2022 (UTC)
• The "overview" section needs wiki links. Terms already linked in the lead should be linked again in the body.
• eDNA can be captured from environmental samples and preserved, extracted – what is the difference betwwen "captured" and "extracted"?
• sequenced, and categorized based on its sequence. – sequenced based on its sequence? What does this mean?
• From this information, detection and classification of species is possible – do you mean "identification"? "Classification" is a huge step further.
• skin, mucous, saliva, sperm, secretions, eggs, feces, urine, blood, roots, leaves, fruit, pollen – why do you list "hair" in the lead but not here?
• age and feeding activity of the organism as well as physiology, life history – age and life history, isn't that the same? Not clear what you mean.
• On hold: I am generally worried about Good Article criterium 1, "well written". The prose does not seems sufficiently clear and easy to follow, and the article structure might not be ideal. I hope the above examples may give an idea about what to look for. If anything is unclear, please let me know. I would suggest that I put the article on hold for now, to give you some time to improve overall readability of the article. Thanks, --Jens Lallensack (talk) 20:32, 2 January 2022 (UTC)

@Jens Lallensack: thank you for those thoughtful comments. I'll address these issues over the next few days. —Epipelagic (talk) 07:10, 3 January 2022 (UTC)

Closing note: Failed GA per request by the author. --Jens Lallensack (talk) 11:06, 6 January 2022 (UTC)

Addressing ref based GA review comments

I was fixing some ref errors in this article; at the same time also cleaned up a bunch of duplicated refs mostly from the lead and cleaned up the selfDNA section, which goes a little way to addressing some of the ref based comments in the GA review above. Amkilpatrick (talk) 14:26, 10 January 2022 (UTC)

Privacy and ethical concerns

The article currently contains only the positive aspects of eDNA. Increasingly, aspects concerning privacy and ethical concerns have been raised.

I'm not an expert in the field but perhaps someone more knowledgeable might add a section (or two sections?) covering such issues. Following are a few sources that discuss such issues:

- https://www.nytimes.com/2023/05/15/science/environmental-dna-ethics-privacy.html

- https://www.pbs.org/newshour/science/analysis-we-shed-our-dna-everywhere-we-go-heres-why-that-raises-privacy-concerns

- https://phys.org/news/2023-05-dna-samples-sand-air-ethical.html

- https://www.science.org/content/article/privacy-concerns-sparked-human-dna-accidentally-collected-studies-other-species

- https://www.vice.com/en/article/88xq4v/human-dna-is-all-over-the-place-raising-privacy-concerns

- https://cosmosmagazine.com/people/ethics/edna-ethical-risks/

- https://www.bbc.co.uk/programmes/m001m4w7 31.51.14.148 (talk) 20:55, 25 May 2023 (UTC)

SedaDNA

This article is mainly about modern environmental DNA. I think the section on SedaDNA (sedimentary ancient DNA) is primarily of interest to people interested in Ancient DNA. I suggest moving the section to that article with a hatnote on this article {{about|modern environmental DNA|ancient sedimentary DNA (SedaDNA)|Ancient DNA}}. Dudley Miles (talk) 19:13, 2 June 2023 (UTC)

History?

Greetings,
In addition to the topics suggested for change by the reviewer, how about information on the history of the technique? I am lost trying to find any here.

• What is the origin of the concept of searching soils for DNA?
• How was it achieved and how long did it take?
• How did the genetics community accept the new technique?
• How far back was DNA found? (I saw where it is 2,000,000 ya Is that true?)

I came here for the history of eDNA and was disappointed.
Thank you for your time, Wordreader (talk) 16:03, 7 April 2024 (UTC)