Evaluating monitoring options for conservation: comparing traditional and environmental DNA tools for a critically endangered mammal

The Science of Nature, Feb 2019

While conservation management has made tremendous strides to date, deciding where, when and how to invest limited monitoring budgets is a central concern for impactful decision-making. New analytical tools, such as environmental DNA (eDNA), are now facilitating broader biodiversity monitoring at unprecedented scales, in part, due to time, and presumably cost, of methodological efficiency. Genetic approaches vary from conventional PCR (cPCR; species presence), to metabarcoding (community structure), and qPCR (relative DNA abundance, detection sensitivity). Knowing when to employ these techniques over traditional protocols could enable practitioners to make more informed choices concerning data collection. Using 12 species-specific primers designed for cPCR, eDNA analysis of the Yangtze finless porpoise (YFP; Neophocaena asiaeorientalis asiaeorientalis), a critically endangered aquatic mammal within the Yangtze River, we validated and optimized these primers for use in qPCR. We tested repeatability and sensitivity to detect YFP eDNA and subsequently compared the cost of traditional (visual and capture) sampling to eDNA tools. Our results suggest cPCR as the least expensive sampling option but the lack of PCR sensitivity suggests it may not be the most robust method for this taxon, predominately useful as a supplementary tool or with large expected populations. Alternatively, qPCR remained less expensive than traditional surveys, representing a highly repeatable and sensitive method for this behaviorally elusive species. Cost comparisons of surveying practices have scarcely been discussed; however, given budgetary constraints particularly for developing countries with limited local oversight but high endemism, we encourage managers to carefully consider the trade-offs among accuracy, cost, coverage, and speed for biodiversity monitoring.

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Evaluating monitoring options for conservation: comparing traditional and environmental DNA tools for a critically endangered mammal

The Science of Nature April 2019, 106:9 | Cite as Evaluating monitoring options for conservation: comparing traditional and environmental DNA tools for a critically endangered mammal AuthorsAuthors and affiliations Chanjuan QuKathryn A. Stewart Open Access Original Paper First Online: 18 February 2019 6 Shares 452 Downloads Abstract While conservation management has made tremendous strides to date, deciding where, when and how to invest limited monitoring budgets is a central concern for impactful decision-making. New analytical tools, such as environmental DNA (eDNA), are now facilitating broader biodiversity monitoring at unprecedented scales, in part, due to time, and presumably cost, of methodological efficiency. Genetic approaches vary from conventional PCR (cPCR; species presence), to metabarcoding (community structure), and qPCR (relative DNA abundance, detection sensitivity). Knowing when to employ these techniques over traditional protocols could enable practitioners to make more informed choices concerning data collection. Using 12 species-specific primers designed for cPCR, eDNA analysis of the Yangtze finless porpoise (YFP; Neophocaena asiaeorientalis asiaeorientalis), a critically endangered aquatic mammal within the Yangtze River, we validated and optimized these primers for use in qPCR. We tested repeatability and sensitivity to detect YFP eDNA and subsequently compared the cost of traditional (visual and capture) sampling to eDNA tools. Our results suggest cPCR as the least expensive sampling option but the lack of PCR sensitivity suggests it may not be the most robust method for this taxon, predominately useful as a supplementary tool or with large expected populations. Alternatively, qPCR remained less expensive than traditional surveys, representing a highly repeatable and sensitive method for this behaviorally elusive species. Cost comparisons of surveying practices have scarcely been discussed; however, given budgetary constraints particularly for developing countries with limited local oversight but high endemism, we encourage managers to carefully consider the trade-offs among accuracy, cost, coverage, and speed for biodiversity monitoring. KeywordsYangtze finless porpoise Environmental DNA Systematic conservation planning  Communicated by: Matthias Waltert Electronic supplementary material The online version of this article ( https://doi.org/10.1007/s00114-019-1605-1) contains supplementary material, which is available to authorized users. Introduction As a discipline, systematic conservation planning (e.g., Margules and Pressey 2000) has now surpassed three decades, and its achievements around the world have been remarkable. Still, the social and political environment in which conservation issues are addressed is highly complex, often forming a nexus between the cost, speed, and accuracy of collecting necessary biodiversity data. Indeed, so much of conservation fundamentally involves choices about where, when and how to make investments, thus requiring organismal information at scales commensurate with both goals and monetary availability. Therefore, there remains a vital need to continually highlight new analytical frameworks, innovations, and advances in our collective understanding and approaches to conservation’s core objectives. Despite the prerequisite for comprehensive monitoring initiatives in conservation programs, a thorough knowledge of organismal distribution and abundance is often prohibitive due largely to difficulties in data collection for hard-to-study taxa (e.g., cryptic, behaviourally elusive, low site fidelity, or rare), difficult to sample locales (e.g., aquatic environments), and affiliated costs, particularly in developing countries (Danielsen et al. 2003). Advancements in biodiversity data monitoring via DNA sampled straight from the environment (without invasively targeting taxa) known as eDNA has recently revolutionized conservation biology. Advocated as a time and cost-effective alternative to traditional methods of biodiversity data monitoring, eDNA is a highly sensitive technology that has been successfully employed for myriad species and goals (e.g., Ficetola et al. 2008; Lodge et al. 2012; Fukumoto et al. 2015; Ma et al. 2015; Dougherty et al. 2016). However, just as surveying methods are varied, so too are eDNA applications, and few studies to date have assessed and compared the cost of these protocols. Applications of eDNA methodology can range from detecting the presence/absence of species with conventional PCR (cPCR) (e.g., Jerde et al. 2011; Dejean et al. 2012; Thomsen et al. 2012; Mahon et al. 2013; Piaggio et al. 2014; Fukumoto et al. 2015) or community constituents via metabarcoding (e.g., Evans et al. 2015; Valentini et al. 2016; Hänfling et al. 2016; Shaw et al. 2016), to quantifying the relative abundance of DNA sequences (proxies for relative species abundance) or increasing detection sensitivity via qu (...truncated)


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Chanjuan Qu, Kathryn A. Stewart. Evaluating monitoring options for conservation: comparing traditional and environmental DNA tools for a critically endangered mammal, The Science of Nature, 2019, pp. 9, Volume 106, Issue 3-4, DOI: 10.1007/s00114-019-1605-1