DNA Metabarcoding of Pollen
“DNA metabarcoding” is the use of genetic markers to taxonomically identify mixed-species samples, using high-throughput DNA sequencing. We got interested in developing methods for DNA metabarcoding of pollen in order to build highly-resolved pollination networks via molecular identification of pollen carried by pollinators, but it also has a range of other interesting and important applications from forensics to provenance identification to paleontology. Our past methods development work on this topic, and our current work on quantitation, have been supported by the Army Research Office. Karen Bell, a former post-doc in our lab and currently a faculty member at the University of Western Australia and CSIRO, is a key collaborator in this work.
This work shows the integration between our DNA metabarcoding work and our network studies—demonstrating for the first time that highly-resolved pollination networks can be constructed by metabarcoding pollen carried by flower visitors. We highlight a number of suggestions for using this technique for network studies.
This review lays out the current status of pollen metabarcoding, including its promise as a technique, its limitations, and key areas for future research.
Quantitative Pollen Metabarcoding
While metabarcoding works well for establishing the presence of particular species, it performs poorly in establishing relative proportions of species in a sample. With funding from the Army Research Office (2017-2020) and in collaboration with Karen Bell (UWA) and Tim Read (Emory), we have just begun a project to develop methods for quantitative pollen metabarcoding, by correcting for isolation, copy number, and amplification biases using both new laboratory assays (with samples designed in a phylogenetic context) and with informatics approaches. We are currently recruiting a post-doc with experience in bioinformatics and statistics to work on this project. In exploring topics like organellar copy number in a phylogenetic context, this work also has interesting potential implications for the evolution of organellar genomes in a phylogenetic context and for transgene containment.
Syrphid Fly Pollen Transport Networks
In work driven by Natasha De Vere (National Botanical Garden of Wales) and her doctoral student Andrew Lucas, we are collaborating on studies focused on understanding the structure and dynamics of syrphid fly pollen transport networks. This work is taking place in Wales, whose entire flora is included in DNA barcode libraries, making it an ideal test case for integrating metabarcoding into ecological studies.