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An analytical framework for estimating aquatic species density from environmental DNA.

ABSTRACT: Environmental DNA (eDNA) analysis of water samples is on the brink of becoming a standard monitoring method for aquatic species. This method has improved detection rates over conventional survey methods and thus has demonstrated effectiveness for estimation of site occupancy and species distribution. The frontier of eDNA applications, however, is to infer species density. Building upon previous studies, we present and assess a modeling approach that aims at inferring animal density from eDNA. The modeling combines eDNA and animal count data from a subset of sites to estimate species density (and associated uncertainties) at other sites where only eDNA data are available. As a proof of concept, we first perform a cross-validation study using experimental data on carp in mesocosms. In these data, fish densities are known without error, which allows us to test the performance of the method with known data. We then evaluate the model using field data from a study on a stream salamander species to assess the potential of this method to work in natural settings, where density can never be known with absolute certainty. Two alternative distributions (Normal and Negative Binomial) to model variability in eDNA concentration data are assessed. Assessment based on the proof of concept data (carp) revealed that the Negative Binomial model provided much more accurate estimates than the model based on a Normal distribution, likely because eDNA data tend to be overdispersed. Greater imprecision was found when we applied the method to the field data, but the Negative Binomial model still provided useful density estimates. We call for further model development in this direction, as well as further research targeted at sampling design optimization. It will be important to assess these approaches on a broad range of study systems.

SUBMITTER: Chambert T

PROVIDER: S-EPMC5869225 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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An analytical framework for estimating aquatic species density from environmental DNA.

Chambert Thierry T Pilliod David S DS Goldberg Caren S CS Doi Hideyuki H Takahara Teruhiko T

Ecology and evolution 20180225 6

Environmental DNA (eDNA) analysis of water samples is on the brink of becoming a standard monitoring method for aquatic species. This method has improved detection rates over conventional survey methods and thus has demonstrated effectiveness for estimation of site occupancy and species distribution. The frontier of eDNA applications, however, is to infer species density. Building upon previous studies, we present and assess a modeling approach that aims at inferring animal density from eDNA. Th ...[more]

PMID: 29607039

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Project description:Rapid population growth, climate change, limited natural resources, and the COVID-19 pandemic contribute to increased global hunger, necessitating intensive efforts to ensure food security and nutrition (FSN). Previous FSN approaches covered some dimensions, but not all, resulting in significant gaps in food security indicators. The Gulf Cooperation Council (GCC) and the Middle East and North Africa (MENA) regions have received less attention in food security studies, thus far necessitating considerable effort to develop an appropriate analytical framework. This study reviewed articles and international reports of FSN indicators, drivers and policies, methods, and models and extracted the challenges and gaps from the global and UAE contexts. The UAE and the world have gaps in FSN drivers, indicators, and methods, necessitating potential solutions to meet future challenges such as rapid population growth, pandemics, and limited natural resources. As a result, we created a newly developed analytical framework that addresses the shortcomings of previous approaches such as sustainable food systems developed by FAO and the Global Food Security Index (GFSI) and covers all aspects of food security. Gaps in knowledge in FSN drivers and policies, indicators, big data, methods, and models were considered in the developed framework, which has specific advantages. The novel developed framework addresses all food security dimensions (access, availability, stability, and utilization), ensuring poverty reduction, food security, and nutrition security while outperforming previous approaches (i.e., FAO and GFSI). The developed framework could be used successfully not only in the UAE and MENA, but also, globally, helping to solve food insecurity and malnutrition for future generations. The scientific community and policymakers should disseminate such solutions to address global food insecurity and ensure nutrition for future generations in the face of rapid population growth, limited natural resources, climate change, and spreading pandemics.Supplementary informationThe online version contains supplementary material available at 10.1007/s10668-023-03032-3.

Dataset Information

An analytical framework for estimating aquatic species density from environmental DNA.

Publications

An analytical framework for estimating aquatic species density from environmental DNA.

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