My research interests

My research interests focus on gaining a better understanding of plant diversity in our natural world, using both flowering plants (angiosperms) and seed plants like cycads and confiers (gymnosperms), as example groups with a personal interest in the cycads (Cycadales). By using modern genetic techniques and the morphology that defines species, my research hopes to gain further insights into the genomic and systematic relationships of both flowering and seed plants. Conservation genomics, systematics, phylogentics and plant evolution developmental genetics are areas of major interest for me and where my research path heads. Though my research I hope to gain a better understanding into the genetic and morphological diversity of all plants on earth and help to untangle their complex evolutionary history to help in the ex-situ botanic garden conservation of these plants for the greater good.

Current research projects

Building the eFlora: Generic and species-level resolution in Fabaceae tribe Mirbelieae using next-generation sequencing.

Australia has a very diverse pea-flowered legume flora with 1,715 native and naturalised species recognised. This project aims genetic sequencing (NGS) to understand generic relationships between species the Pultenaea alliance (Fabaceae tribe Mirbelieae; poison peas and their relatives). Mirbelieae includes 44% of Australia‘s peas in 24 genera and around 754 currently recognised species. The project will use DNA sequencing to sample key species that will help to understand relationships between genera and species. The research will not only help to differentiate species but will provide updates to the eFlora to help other differentiate them.

Developing new methods for DNA barcoding of Encephalartos in South Africa.

The project aims to develop new methods to genotype species and populations of South African cycad genus Encephalartos. Using RADseq methods the project will aim to provide an accurate species level identification and determine the origin of wild Encephalartos specimens that have been confiscated by customs or recovered from illegal trade, and facilitate their return to their original populations. 

Previous research projects

Exploring new approaches for conservation genetics of the genus Cycas L. (Cycadaceae) in Australia.

This project explores new approaches for the conservation genetics of the genus Cycas in Australia, in particular using next generation sequencing methods. My research is focused on understanding the genetic and genomic diversity of cycads, a group of plants with an ancient fossil record. More specifically, this work involves the genus Cycas (Cycadaceae), which is the most diverse group of the cycads. My PhD project aims to apply new approaches such as next generation sequencing technologies to better understand the genetic diversity in wild populations of Cycas in Australia. The project will also compare the complete genetic reserves of wild populations with the ex-situ conservation collections in order to understand how the cultivated collections represent the genetic diversity of the natural wild populations. Ultimately the project aims to create a conservation strategy to best preserve natural populations of Cycas.

Published work

Clugston. J. A. R., R. L. Barrett, D. J. Murphy, M. A. M. Renner, P. H. Weston, L. G. Cook, P. C. Jobson, B. J. Lepschi and M. D. Crisp. Resolving relationships in the radiation of Australia’s largest pea clade (Fabaceae tribe Mirbelieae) with target-capture sequencing. Annuals of Botany (submitted 23283 MS).

Barrett, R. L., J. A.R. Clugston, D. E. Albrecht, L. Elkan, J. R. Hosking, P. C. Jobson, S. F. McCune, A. E. Orme, R. L. Palsson, M. A. M. Renner, C. Wardrop and P. H. Weston. Revision of the Pultenaea setulosa species complex (Fabaceae: Mirbelieae) including fourteen new species. Australian Systematic Botany (submitted SB23014).

Stewart R. D., J. A. R. Clugston, J. Williamson, H. Niemand, D. Little, M. van der Bank. (2022). Creating a better foundation for understanding the species diversity and phylogenetics of the genus Encephalartos Lehm. (Zamiaceae). South African Journal of Botany. 152, 165–173.

Calonje, M., & Clugston, J. A. R. (2022). Proposal to conserve the name Cycas riedlei Fisch. Ex Gaudich. (Macrozamia riedlei) against C. riedlei Dum. Cours. (Cycadaceae). Taxon 71(5), 1113–1115.

Telford, I. I., Clugston, J. A. R., & Barrett, R. L. (2022). Pultenaea williamsii (Fabaceae: Mirbelieae), a new species endemic to the New England Tableland Bioregion of New South Wales. Telopea 25, 165–171.

Renner, M. A., Barrett, R. L., Clarke, S., Clugston, J. A. R., Wilson, T. C., & Weston, P. H. (2022). Morphological and molecular evidence refute a broad circumscription for Pultenaea glabra (Fabaceae: Mirbelieae), with implications for taxonomy, biogeography, and conservation. Australian Systematic Botany 35(3), 225–277.

Clugston, J. A. R., G. J. Kenicer, M. M. Rusham, M. J. Henwood, R. Milne, and N. S. Nagalingum. Next-generation population genetics in Australian Cycas sheds light on the origins of C. armstrongii and C. maconochiei subsp. maconochiei. in prep.

Clugston, J. A. R., & Kenicer, G. J. (2022). Sexing cycads—a potential saviour. Nature Plants, 1-2.

Clugston, J. A. R., Ruhsam, M., Kenicer, G. J., Henwood, M., Milne, R., & Nagalingum, N. S. (2022). Conservation genomics of an Australian cycad Cycas calcicola, and the Absence of Key Genotypes in Botanic Gardens. Conservation Genetics, 1-17.

Barrett, R. L., Clugston, J. A. R., Cook, L. G., Crisp, M. D., Jobson, P. C., Lepschi, B. J., & Weston, P. H. (2021). Understanding Diversity and Systematics in Australian Fabaceae Tribe Mirbelieae. Diversity, 13(8), 391.

Clugston, J. A. R., R. R. Milne, G. J. Kenicer, I. Overcast, N. S. Nagalingum, 2019. RADseq as a valuable tool for plants with large genomes—a case study in cycads. Molecular Ecology Resources. 19, 1610-1622.

Tucker Lima, J. M., N. M. Caruso, J. A. R. Clugston, K. A. Kainer. 2018. Landscape change alters reproductive phenology and sex expression in Attalea palms (Arecaceae) of southwestern Amazonia. Plant Ecology, 219(10), 1225-1245.

Vovides A. P., J. A. R. Clugston, J. S. Gutiérrez-Ortegad, M. A.Pérez-Farrerae, M. Y. Sánchez-Tinoco and S. Galicia, 2018. Epidermal morphology and leaflet anatomy of Dioon (Zamiaceae) with comments on climate and environment. Flora, 239, 20–44.

Clugston, J. A.R., M. P. Griffith, M. A. Calonje, C. E. Husby, G. J. Kenicer, D. P. Little, and D. Wm. Stevenson, 2018. Reproductive Phenology of Zamia L. – a comparison between wild cycads and their cultivated counter-parts. Botanical Review, Proceedings of the 9th International Conference on Cycad Biology. Memoirs of The New York Botanical Garden, 117, 433–462.

Clugston, J. A. R., C. E. Jeffree, A. Ahrends and R. R. Mill, 2017. Do Environmental Factors Affect the Taxonomic Reliability of Leaf Cuticular Micromorphological Characters? A Case Study in Podocarpaceae, Edinburgh Journal of Botany, 74(3), 299–343.

Clugston, J. A. R., M. P. Griffith, G. J. Kenicer, C. E. Husby, M. A. Calonje, D. Wm.  Stevenson & D. P. Little, 2016. Zamia (Zamiaceae) phenology in a phylogenetic context: does in situ reproductive timing correlate with ancestry? Edinburgh Journal of Botany, 73, 345–370.

Clugston, J. A. R., "Student Project: Data Capture and Taxonomic Determination of Cycadales at the Royal Botanic Garden Edinburgh." Sibbaldia, The Journal of Botanic Garden Horticulture, 2010: 11-30 (No.8).

Abstracts 

Clugston, James A. R., Patrick M. Griffith, Gregory J. Kenicer, Damon P. Little, and Dennis Wm. Stevenson. "Phenology of Zamia L.-phylogentic and biogeographical insights." Journal of Fairylake Botanical Garden 10, no. 3 (2011): 40.