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Opportunities and inherent limits of using environmental DNA for population genetics


Couton, Marjorie; Viard, Frédérique; Altermatt, Florian (2023). Opportunities and inherent limits of using environmental DNA for population genetics. Environmental DNA, 5(5):1048-1064.

Abstract

Molecular techniques using DNA retrieved from community or environmental samples, in particular environmental DNA (eDNA), are becoming increasingly popular for detecting individual species, assessing biodiversity, and quantifying ecological indices. More recently, eDNA has also been proposed as a template for population genetics, and several studies have already tested the feasibility of this approach, mostly looking at vertebrate species. Their results along with general opportunities offered by these types of “community‐based” samples, such as the possibility to target multiple species at the same time, have generated great enthusiasm and expectations for using eDNA in population genetics. However, not every aspect of population genetics can be addressed by eDNA‐based data and some inherent limitations may challenge its conclusions. Here, we firstly review the state of current knowledge of DNA retrieved from environmental and community samples for population genetics. Then, focusing on eDNA, we summarize the opportunities but also detail four main limitations of its use for population‐level inferences, namely, (1) the difficulty to retrieve a species‐specific dataset, (2) the potential lack of correlation between observed and true allelic frequencies, (3) the loss of individual information in multi‐locus genotyping and linkage between loci, and (4) the uncertainty about the individuals contributing to the sampled DNA pool (e.g., number, life‐stage, or sex). Some of these limitations might be overcome with the development of new technologies or models that account for the specificities of eDNA. Others, however, are inherent, and their effect on the inferences must be thoroughly evaluated. The possibility of gaining insights into genetic diversity and population structure from DNA retrieved from community and environmental samples is appealing for scientists, conservation managers, and other practitioners. Yet, to avoid false expectations and incorrect inferences, it is imperative that these limitations are known and considered alongside the opportunities and advantages.

Abstract

Molecular techniques using DNA retrieved from community or environmental samples, in particular environmental DNA (eDNA), are becoming increasingly popular for detecting individual species, assessing biodiversity, and quantifying ecological indices. More recently, eDNA has also been proposed as a template for population genetics, and several studies have already tested the feasibility of this approach, mostly looking at vertebrate species. Their results along with general opportunities offered by these types of “community‐based” samples, such as the possibility to target multiple species at the same time, have generated great enthusiasm and expectations for using eDNA in population genetics. However, not every aspect of population genetics can be addressed by eDNA‐based data and some inherent limitations may challenge its conclusions. Here, we firstly review the state of current knowledge of DNA retrieved from environmental and community samples for population genetics. Then, focusing on eDNA, we summarize the opportunities but also detail four main limitations of its use for population‐level inferences, namely, (1) the difficulty to retrieve a species‐specific dataset, (2) the potential lack of correlation between observed and true allelic frequencies, (3) the loss of individual information in multi‐locus genotyping and linkage between loci, and (4) the uncertainty about the individuals contributing to the sampled DNA pool (e.g., number, life‐stage, or sex). Some of these limitations might be overcome with the development of new technologies or models that account for the specificities of eDNA. Others, however, are inherent, and their effect on the inferences must be thoroughly evaluated. The possibility of gaining insights into genetic diversity and population structure from DNA retrieved from community and environmental samples is appealing for scientists, conservation managers, and other practitioners. Yet, to avoid false expectations and incorrect inferences, it is imperative that these limitations are known and considered alongside the opportunities and advantages.

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Additional indexing

Item Type:Journal Article, not_refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Evolutionary Biology and Environmental Studies
08 Research Priority Programs > Global Change and Biodiversity
Dewey Decimal Classification:570 Life sciences; biology
590 Animals (Zoology)
Scopus Subject Areas:Life Sciences > Ecology, Evolution, Behavior and Systematics
Physical Sciences > Ecology
Life Sciences > Genetics
Uncontrolled Keywords:Genetics, Ecology, Ecology, Evolution, Behavior and Systematics
Language:English
Date:1 September 2023
Deposited On:24 Jan 2024 09:17
Last Modified:29 Jun 2024 03:31
Publisher:Wiley-Blackwell Publishing, Inc.
ISSN:2637-4943
OA Status:Gold
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1002/edn3.448
Project Information:
  • : FunderBundesamt für Umwelt
  • : Grant ID
  • : Project Title
  • : FunderTotal Foundation
  • : Grant ID
  • : Project Title
  • : FunderUniversität Zürich
  • : Grant ID
  • : Project Title
  • : FunderSNSF
  • : Grant ID31003A_173074
  • : Project TitleRiverDNA: uncovering fundamental biodiversity in riverine systems using environmental DNA
  • Content: Published Version
  • Language: English
  • Licence: Creative Commons: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)