A comparison of eDNA to camera trapping for assessment of terrestrial mammal diversity.

Kevin Leempoel,Trevor Hebert,Elizabeth A Hadly

doi:10.1098/rspb.2019.2353

Kevin Leempoel, Trevor Hebert + Show 1 more

Open Access

https://doi.org/10.1098/rspb.2019.2353

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Abstract

Before environmental DNA (eDNA) can establish itself as a robust tool for biodiversity monitoring, comparison with existing approaches is necessary, yet is lacking for terrestrial mammals. Moreover, much is unknown regarding the nature, spread and persistence of DNA shed by animals into terrestrial environments, or the optimal experimental design for understanding these potential biases. To address some of these challenges, we compared the detection of terrestrial mammals using eDNA analysis of soil samples against confirmed species observations from a long-term (approx. 9-year) camera-trapping study. At the same time, we considered multiple experimental parameters, including two sampling designs, two DNA extraction kits and two metabarcodes of different sizes. All mammals regularly recorded with cameras were detected in eDNA. In addition, eDNA reported many unrecorded small mammals whose presence in the study area is otherwise documented. A long metabarcode (≈220 bp) offering a high taxonomic resolution, achieved a similar efficiency as a shorter one (≈70 bp) and a phosphate buffer-based extraction gave similar results as a total DNA extraction method, for a fraction of the price. Our results support that eDNA-based monitoring should become a valuable part of ecosystem surveys, yet mitochondrial reference databases need to be enriched first.

Highlights

Biodiversity loss due to human activities has been documented by numerous studies and calls for improved evaluations of species diversity, distribution and abundance [1,2]
Our study was conducted at the Jasper Ridge Biological Preserve (JRBP), California, USA, where we took advantage of a long-term camera-trapping effort initiated in 2009
We identified 25 molecular operational taxonomic units (MOTUs) with 16S and 44 MOTUs with 12S but many were removed or regrouped during our data processing pipeline

Summary

Introduction

Biodiversity loss due to human activities has been documented by numerous studies and calls for improved evaluations of species diversity, distribution and abundance [1,2]. Distinguishing cryptic species (i.e. species that look identical but that are genetically distinct) remains an arduous task because surveys are based either on photographs or measurements of phenotypic traits, requiring substantial expertise and comprehensive sampling [5]. Comprehensive comparisons of species diversity identified through eDNA or ingested DNA (iDNA) alongside traditional surveys are required prior to using eDNA for biodiversity monitoring across ecosystems [4]. These comparisons are, rare, and usually conducted in aquatic ecosystems [12,13]. How does experimental design affect our ability to perform 2 biodiversity monitoring using eDNA?

Are eDNA and camera-trapping results comparable?

Methods

Results

Discussion