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.

Key Publications

Dicks LV, Viana B, Bommarco R, Brosi BJ, del Coro Arizmendi M, Cunningham SA, Galetto L, Hill R, Lopes AR, Pires C, Taki H, Cooper D, Potts SG. Ten policies to protect pollinators. Science, 2016. 354, 975–976.
Bell KL, Fowler J, Burgess KS, Dobbs EK, Gruenewald D, Lawley B, Morozumi C, Brosi BJ. Applying pollen DNA metabarcoding to the study of plant-pollinator interactions. Applications in Plant Sciences, 2017. 5(6): 1600124

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.

Brosi, BJ, Niezgoda K, Briggs HM.. Experimental species removals impact the architecture of pollination networks. Biology Letters, 13: 20170243

Most network simulation studies exploring the consequences of species losses assume that network structure stays fixed after species losses. In these replicated field experiments we show that network structure is altered, in ways that can be predicted from basic ecological theory.

Dynes, T.L., J.C. De Roode, J.I. Lyons, J.A. Berry, K.S. Delaplane, B.J. Brosi. Fine scale population genetic structure of Varroa destructor, an ectoparasitic mite of the honey bee (Apis mellifera). Apidologie, 2017. 48(1): 93-101

This is the first work to use population genetic approaches to understand patterns of gene flow and potentially transmission in Varroa mites, the single largest cause of honey bee colony loss worldwide.

Brosi BJ, Delaplane KS, Boots M, De Roode JC. Ecological and evolutionary approaches to managing honey bee disease.. Nature Ecology and Evolution, 2017. 1, 1250–1262

This review lays out why we need to incorporate ecological and evolutionary considerations into the management of honey bee disease, including developing the idea that current management techniques may actually be selecting for more-virulent parasites and pathogens.

Strauss SH, Jones KN, Lu H, Petit JH, Klocko AH, Brosi BJ, Betts MG, Needham MD, Fletcher RJ. Impacts of Flowering Modification on Biodiversity in Forest Plantations. New Phytologist, 2017. 213: 1000–1021
Bell, K.L., K.S. Burgess, N. De Vere, A. Gousse, A. Keller, R. Richardson, B.J. Brosi. DNA metabarcoding of pollen: progress and prospects. Genome, 2016. 59(9): 629-640

This review lays out the current status of pollen metabarcoding, including its promise as a technique, its limitations, and key areas for future research.

B.J. Brosi. Pollinator Specialization: from the Individual to the Community. New Phytologist, 2016. 210: 1190–1194. DOI: 10.1111/nph.13951

This review lays out why foraging choices in pollinators, at multiple scales, can drive important system properties including diversity-functioning relationships.

Valdovinos, F.S., B.J. Brosi, H.M. Briggs, P. Moisset de Espanés, R. Ramos-Jiliberto, N.D. Martinez.. Adaptive foraging interacts with network structure to stabilize mutualistic networks. Ecology Letters, 2016. 19: 1277–1286.

This paper integrates modeling and our field data from Colorado, and shows that “adaptive foraging”—behavioral plasticity in foraging intensity on different resources—is key for stabilizing pollination networks, but has different effects in networks with different structures.

Ayers, C.A., P.R. Armsworth, B.J. Brosi. Determinism as a statistical metric for trapline foraging and other recurrent behaviors. Behavioral Ecology and Sociobiology, 2015. 69:1395–1404

Trapline foraging is a key behavioral tactic used by pollinators and many other groups of animals. This work develops a new method for measuring traplining—which has been notoriously challenging to quantify—borrowing quantitative tools from statistical physics.

Suni SS, Brosi, BJ (2012). Population genetics of orchid bees in a fragmented tropical landscape. Conservation Genetics, 13: 323-332
Anderson, LM, TM Dynes, JA Berry, KS Delaplane, LLMcCormick, and BJ Brosi. 2014. Distinguishing feral and managed honeybees (Apis mellifera) using stable carbon isotopes. Apidologie, 45(6): 653-663
Tallis, H, J Lubchenco, … BJ Brosi.2014.. Working together: A call for inclusive conservation. Nature, 515(7525): 27–28.
Bee and wildflower


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.