Opportunities and inherent limits of using environmental DNA for population genetics

• Published in: Environmental DNA (Hoboken, N.J.) Vol. 5; no. 5; pp. 1048 - 1064
• Main Authors: Couton, Marjorie, Viard, Frédérique, Altermatt, Florian
• Format: Journal Article
• Language: English
• Published: Hoboken John Wiley & Sons, Inc 01.09.2023; John Wiley & Sons Inc; Wiley
• Subjects: Biodiversity; Biodiversity and Ecology; conservation of natural resources; Deoxyribonucleic acid; DNA; DNA barcoding; DNA structure; Ecology; Environmental DNA; Environmental Sciences; gene flow; Genetic diversity; genetic markers; genetic models; Genetic testing; Genetics; Genotyping; Life Sciences; Loci; New technology; Organisms; phylogeography; Population genetics; population statistics; Population structure; Population studies; Populations and Evolution; Vertebrates; gene flow; genetic diversity; DNA barcoding; conservation of natural resources; genetic markers; genetic models; population statistics; phylogeography
• ISSN: 2637-4943; 2637-4943
• DOI: 10.1002/edn3.448

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. We present here a review of the state of current knowledge of the use of DNA retrieved from environmental and community samples for population genetics. Then, focusing on environmental DNA (eDNA), we summarize the opportunities but also detail four main limitations of its use for population‐level inferences. Although the use of eDNA is appealing for scientists, conservation managers and other practitioners, it is imperative that its limitations are known and considered to avoid false expectations and incorrect inferences.