We have posted a couple detailed new protocols describing our methods to sequence key mammalian DNA barcodes. 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. They can be found on our lab's protocol page.

Beginning in June, we have increasingly made our internal lab methods publicly visible on the "Protocols" section of our webpage. We began with some of the most frequently requested protocols that speak to the unique strengths of our lab's work and experience, featuring field-to-lab protocols for collecting and banking dietary samples, parasite samples, and plant barcode samples. We have expanded to include...

Over the past couple of years, a lot of things have changed. Some of those changes have brought improvements to the way we share the software and data that we generate in the lab, necessitated in part by the growing popularity of our work to a point that we recognized a substantial benefit to enhancing our commitment to easy access and open-source principles. 

To make it easier to find and access our most in-demand repositories -- often spread across a variety of platforms including GitHub, Zenodo, NCBI, BOLD, etc. -- we have created a main landing page on the website where we have curated a mix of both recent and timeless contributions to the field. Check it out!

You might also want to check out our lab's main GitHub repository, where we are increasingly making our projects publicly available so you can benefit from any updates we've made since posting a version of record for the code with a prior publication (e.g., a static record with a Zenodo DOI). 

I will periodically post updates to this blog in order to highlight and summarize important updates to help ensure the community is aware, but we will no longer be using these pages to share data or code directly as we have in the past.

By Bethan Littleford-Colquhoun

A huge debt of gratitude to Beth for organizing a google drive folder that shares our strategy for initial processing of dietary DNA metabarcoding data. This directory provides template documents and code that we use to download paired-end read data from our dietary metabarcoding workflows, assemble forward and reverse reads, perform initial quality controls, and evaluate sequencing success. There is also a tutorial for how to upload sample data to SRA for archiving, which we have started to do routinely. Some details are specific to our dietary analysis sequencing workflow and/or the specific sequencing service that we use, plus we have particular sample naming schemes that we use, but it should be pretty straightforward to adapt for a variety of similar goals.

By Hannah Hoff

We have been doing a lot of plant DNA barcoding to build a library for the plants of the Greater Yellowstone Ecosystem. In the process, we have done some refinement to our lab's DNA barcoding protocols to increase clarity, efficiency, and reproducibility. Updated links to these protocols are available on the lab's wiki under the "Plant Barcoding" section for: trnL, rbcL, matK, and trnH-psbA markers.