Standard Protocol

Sampling Kit

GMP sampling kit

CBG provides a standard sampling kit to all GMP participants. This includes a brand new Townes style Malaise trap and typically a year’s worth of collection bottles. Partners provide ethanol for killing and preserving samples and are responsible for changing the collection bottle once every week for the duration of the flight season.

Analytical Workflow

All collection bottles are shipped for subsequent processing at CBG. Samples are accessioned, specimens were identified to order, arrayed, labeled, databased, and tissue-sampled for genetic analysis (Figure 1). All arthropods are barcoded, with the exception of a few very common species of Collembola, where only a few individuals from each trap sample were analyzed. Standard barcoding protocols (http://ccdb.ca/resources.php) were followed to recover the barcode region of cytochrome c oxidase subunit I (COI) gene. The barcode sequences, specimen images and collateral data are uploaded to the Barcode of Life Data Systems (BOLD; www.boldsystems.org) under the ‘Global Malaise Program’ campaign. Barcoded specimens are assigned to an existing or new Barcode Index Number (BIN), a proxy for a formal Linnean species name, as outlined by Ratnasingham & Hebert (2013). Identifications were assigned by the BOLD-ID Engine where possible, allowing preliminary species inventories to be completed for each location and facilitating comparisons among them.

Schematic diagram showing specimen workflow. Front end processing begins with field collecting (A) and proceeds through to archiving of specimens (I). Laboratory analysis begins with tissue lysis (J) through to sequence analysis (AA). The informatics workflow includes both manual (AB) and auto sequence assembly (S), and finishes with BIN assignments and subsequent imaging of each BIN (AD).

Reports

Reports are generated upon completion of analysis for a single GMP site. They include a taxonomy list, image library, neighbor-joining tree, and different comparisons with other analyzed GMP locations. The whole program moves forward through collaborative efforts where each country is creating a species inventory and barcode library for itself but shared BINs between countries therefore allow for concurrent identifications between collections.