Fig 1.
Biochemical protocols at the website DNA Barcoding 101 (www.dnabarcoding101.org) and bioinformatics tools at DNA Subway (www.dnasubway.org) support all parts of the workflow. (A) Participants collected samples and extracted genomic DNA, generated DNA barcodes using PCR, verified the correct size by gel electrophoresis and sent amplicons for automated sequencing. Sequence data was uploaded to the internet-based DNA barcoding bioinformatics pipeline DNA Subway, and participants assembled contigs, compared them to additional sequences and analyzed sequence data for potential export to GenBank. (B) Trace file of a DNA sequence from a local ant sample. (C) DNA reads are paired and manually edited to create consensus sequence. (D) Top BLAST hits for an ant consensus sequence identifying it as Tetramorium caespitum. (E) DNA Subway integrated export function for novel DNA barcodes to GenBank. (F) User-friendly DNA Subway interface. (G) DNA Subway’s “Blue Line” for DNA barcoding and phylogenetics allows for sequence editing, performing a BLAST search, and phylogenetic tree building on an intuitive, open-source platform.
Fig 2.
Sampling sites for this study.
Samples were obtained at Marine Park (Brooklyn, New York, USA) in two localities: at a restored, more natural habitat (# 1 above) and an unrestored, disturbed habitat (#2 above). The figure was prepared based on data available from the U.S. Geological Survey Department of the Interior (USGS) public domain (USGS-viewer.nationalmap.gov) and edited by Chun-hua Yang, DNALC.
Fig 3.
Overview of invertebrates identified by this project, organized by taxonomic level.
The vast majority of the animal samples belonged to the phylum Arthropoda (n = 63; 90% of collected animals). Of those 63 samples, most were from the Insecta class (n = 47; 67.1% of collected animals) in the Hymenoptera (n = 30; 42.8% of collected animals) and Diptera (n = 9; 12.8% of collected animals) orders. Taxonomic groups in legends are organized from largest to smallest.
Fig 4.
Overview of plants identified by this project, organized by taxonomic level.
Of the 116 collected and identified plants the majority were in the Asterales (n = 32; 27.6% of total plants) and Poales (n = 28; 24.1% of total plants) orders, with the highest number of species within each order falling in the Asteraceae (n = 32; 27.6% of total plants) and Poaceae families (n = 28; 24.1%). Taxonomic groups in legends are organized from largest to smallest.
Table 1.
Overview of the twelve novel DNA barcodes generated by the participants of the Urban Barcoding Project Institute at GESC in the summers of 2014 and 2015.
Table 2.
List of ant samples, and their corresponding morphological and DNA barcoding identifications.