eDNAPlus: A Unifying Modeling Framework for DNA-based Biodiversity Monitoring

	eDNAPlus: A Unifying Modeling Framework for DNA-based Biodiversity Monitoring
	Diana, A; Matechou, E; Griffin, J; Yu, DW; Luo, MJ; Tosa, M; Bush, A; Griffiths, RA
	2024
发表期刊	J AM STAT ASSOC
ISSN	0162-1459
摘要	DNA-based biodiversity surveys, which involve collecting physical samples from survey sites and assaying them in the laboratory to detect species via their diagnostic DNA sequences, are increasingly being adopted for biodiversity monitoring and decision-making. The most commonly employed method, metabarcoding, combines PCR with high-throughput DNA sequencing to amplify and read DNA barcode sequences, generating count data indicating the number of times each DNA barcode was read. However, DNA-based data are noisy and error-prone, with several sources of variation, and cannot alone estimate the species-specific amount of DNA present at a surveyed site (DNA biomass). In this article, we present a unifying modeling framework for DNA-based survey data that allows estimation of changes in DNA biomass within species, across sites and their links to environmental covariates, while for the first time simultaneously accounting for key sources of variation, error and noise in the data-generating process, and for between-species and between-sites correlation. Bayesian inference is performed using MCMC with Laplace approximations. We describe a re-parameterization scheme for crossed-effects models designed to improve mixing, and an adaptive approach for updating latent variables, which reduces computation time. Theoretical and simulation results are used to guide study design, including the level of replication at different survey stages and the use of quality control methods. Finally, we demonstrate our new framework on a dataset of Malaise-trap samples, quantifying the effects of elevation and distance-to-road on each species, and produce maps identifying areas of high biodiversity and species DNA biomass. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
收录类别	SCI
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/14650
专题	科研部门_生态学与环境保护中心（俞维理）
推荐引用方式 GB/T 7714	Diana, A,Matechou, E,Griffin, J,et al. eDNAPlus: A Unifying Modeling Framework for DNA-based Biodiversity Monitoring[J]. J AM STAT ASSOC,2024.
APA	Diana, A.,Matechou, E.,Griffin, J.,Yu, DW.,Luo, MJ.,...&Griffiths, RA.(2024).eDNAPlus: A Unifying Modeling Framework for DNA-based Biodiversity Monitoring.J AM STAT ASSOC.
MLA	Diana, A,et al."eDNAPlus: A Unifying Modeling Framework for DNA-based Biodiversity Monitoring".J AM STAT ASSOC (2024).

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文件名称/大小	文献类型	版本类型	开放类型	使用许可
DG2025042101.pdf（3576KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	请求全文