​The first public release of data from the HelmBank project is now live with Release R1. This release provides a new set of voucher-linked parasite DNA barcode records designed to improve how helminths are detected and identified from wildlife. This release adds 45 barcodes from 20 newly sequenced specimens with data for the markers COI, 16S, and ITS. Release R1 is part of a larger, growing, and actively curated collection of parasite specimens from wildlife. It currently focuses on the helminth parasites of Neotropical mammals, but coverage is quickly expanding to include a broader array of host taxa.

We have posted detailed new protocols describing our methods to sequence key mammalian DNA barcodes. They can be found together with a growing number of field and lab protocols on the Kartzinel Lab's centralized protocol page.

You will find protocols for both the D-loop of the mitochondrial control region and the 16S marker are useful for identifying a diversity of mammals, and can be routinely amplified from degraded material such as fecal DNA. We have frequently used these protocols to confirm the identity of mammals in studies involving dietary DNA metabarcoding and/or host-microbiome interactions. They are also very useful for phylogenetic analyses. We have used various polymerases over the years, so these protocols may depart slightly from previously published versions (e.g., Kartzinel et al. 2019 PNAS). However, they reflect our current state-of-the-art strategy for routine work and should be generally more cost or time effective as a result of the changes. 

Featured Software from the Kartzinel Lab: Geographic Coverage of DNA Barcodes. The inaugural code repository to be highlighted in our Featured Software section of the Software & Data page presents the Quarto Code Book published in association with our Molecular Ecology Review Paper, "Global Availability of Plant DNA Barcodes as Genomic Resources to Support Basic and Policy-Relevant Biodiversity Research" can be easily modified to evaluate the geographic coverage of other data sets. Although the featured code emphasizes geographic coverage from our work in Yellowstone National Park...

One great application of DNA barcodes is the ability to generate accurate and relevant phylogenetic trees for ecological and evolutionary analyses. There are lots of ways to do this, but not all of them may be necessary or relevant to your end goals. What do you need to know before you get started? This post provides a simple road map that you can follow to decide whether and how to construct a phylogeny using DNA barcode data for your research.