Biodiversity genomics is so much more than just checklists (but those are important too)!  It's a synthesis of field work, molecular biology techniques, and genomics tools used to answer questions about how communities change over space and time and treatment conditions.  The biodiversity genomics toolkit is varied and we pick our tools according to the breadth of the question we need to answer and the level of resolution we need to answer our questions.   We ask questions like, how is the community changing across a gradient and what factors are driving the changes we observe?  We answer those questions through careful sampling in the field and the use of DNA-methods like DNA metabarcoding, metagenomics, and metatranscriptomics.  Teams are comprised of people who love field work, wet lab work, bioinformatics, computational biology, and/or data analysis.  

The field of molecular ecology uses molecular biology tools and the resulting genetic data to answer questions about how organisms interact with each other and the environment.  Conventional sampling approaches include individual specimen collections or soil samples.  The soil can be diluted and plated out on a nutritious substrate so that the fungi can grow, individuals isolated, and pure cultures established.  Pure cultures are crucially important to observe the microscopic characters used for identification, for conducting functional assays (ex. screening for antibiotics or enzyme activity) and for growing up enough material for genome sequencing.  A genome sequence is like the blue-print for a fungus.  It contains the instructions for how to build a fungus and codes for the enzymes that are secreted and used to break down a substrate for absorption (most fungi live in or on their food).  Genome sequences can provide insight into fungal lifestyle and ecology and can be the basis for the development of molecular probes/primers to detect/enrich for similar fungi directly from bulk environmental samples like soil, water, or even air!  For example, at the Royal Ontario Museum laboratory for molecular systematics I used culture-free DNA-based amplicon sequencing to discover numerous cryptic fungal lineages from soil, sometimes referred to as 'dark matter' fungi.  One of these lineages is now known as the Archaeorhizomycetes.  As a part of this work I also used a chromosome-walking technique to generate the data to show how these newly discovered fungi were globally widespread.  

Bioinformatics is an interdisciplinary field that develops computational methods and software to analyze biological data.  To facilitate large-scale analyses of multi-marker data, I've developed numerous curated reference sets.  Each of these sets have also been trained to work with a naive Bayesian classifier to provide a taxonomic assignment with a measure of confidence.  I started this work in the Golding Bioinformatics and Computational Biology lab at McMaster University and have been maintaining and expanding these resources ever since.  My latest project is MetaWorks, a multi-marker metabarcode pipeline.  Unlike most bioinformatic pipelines, MetaWorks is meant to support an array of popular markers used to target bacteria, fungi, diatoms, and animals like arthropods and fish.  Multiple workflows are provided.