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

Chanjuan Qu,Kathryn A Stewart

doi:10.1007/s00114-019-1605-1

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.

Highlights

As a discipline, systematic conservation planning (e.g., Margules and Pressey 2000) has surpassed three decades, and its achievements around the world have been remarkable
Applications of environmental DNA (eDNA) methodology can range from detecting the presence/absence of species with conventional PCR (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 or increasing detection sensitivity via quantitative PCR (e.g., Takahara et al 2012; Goldberg et al 2013; Pilliod et al 2013; Klymus et al 2015; Laramie et al 2015; Balasingham et al 2017)
Using 12 published Yangtze finless porpoise (YFP) primers pairs validated for use in conventional PCR (cPCR) (Ma et al 2016), we optimized quantitative PCR (qPCR) protocols for use in eDNA surveying

Summary

Introduction

Systematic conservation planning (e.g., Margules and Pressey 2000) has surpassed three decades, and its achievements around the world have been remarkable. 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, in developing countries (Danielsen et al 2003). 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). It is difficult to discern when and how to match appropriate sampling protocols with conservation goals in the most cost-effective manner; this understanding could propel the entire field of conservation biology forward and galvanize eDNA as a tractable tool for managers

Methods

Results

Conclusion