Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol.

Jeremy A Miller,Kevin K Beentjes,Steven Ijland,Peter Van Helsdingen

doi:10.3897/zookeys.365.5787

Abstract

We report initial results from an ongoing effort to build a library of DNA barcode sequences for Dutch spiders and investigate the utility of museum collections as a source of specimens for barcoding spiders. Source material for the library comes from a combination of specimens freshly collected in the field specifically for this project and museum specimens collected in the past. For the museum specimens, we focus on 31 species that have been frequently collected over the past several decades. A series of progressively older specimens representing these 31 species were selected for DNA barcoding. Based on the pattern of sequencing successes and failures, we find that smaller-bodied species expire before larger-bodied species as tissue sources for single-PCR standard DNA barcoding. Body size and age of oldest successful DNA barcode are significantly correlated after factoring out phylogenetic effects using independent contrasts analysis. We found some evidence that extracted DNA concentration is correlated with body size and inversely correlated with time since collection, but these relationships are neither strong nor consistent. DNA was extracted from all specimens using standard destructive techniques involving the removal and grinding of tissue. A subset of specimens was selected to evaluate nondestructive extraction. Nondestructive extractions significantly extended the DNA barcoding shelf life of museum specimens, especially small-bodied species, and yielded higher DNA concentrations compared to destructive extractions. All primary data are publically available through a Dryad archive and the Barcode of Life database.

Highlights

The DNA barcoding enterprise has demonstrated its utility for contributing to studies of both well-known and poorly-known taxonomic communities
We looked for a relationship between 1) body size and 2) years since collection against DNA concentration and DNA barcode sequencing success rates for specimens included in the time series study based on both destructive and nondestructive extraction
Larger species have a longer DNA barcoding shelf life than smaller species under museum collection conditions, at least using a single pair of primers to amplify the entire ~650 base pair region in one reaction

Summary

Introduction

The DNA barcoding enterprise has demonstrated its utility for contributing to studies of both well-known and poorly-known taxonomic communities. The focus of this research is to develop a DNA barcode library for a well-known fauna: Dutch spiders. The list of spider species recorded from the Netherlands, which stands as of this writing at 644, has been extensively documented and periodically updated through the Fauna Europaea database (Helsdingen 1999, 2013). The specimens necessary to build such a library come from collections, either fresh material or natural history museums. The national natural history collection for the Netherlands is curated at the Naturalis Biodiversity Center. Our goal is to characterize which specimens in the collection are or are not likely to yield a successful DNA barcode sequence, and to use this knowledge to efficiently build a barcode library based on a combination of fresh and museum specimens

Objectives

Methods

Results

Conclusion