The Birch Lab conduct plant systematics and historical biogeographic research investigating the evolutionary relationships of plant and fungal lineages.
We reconstruct branches of the plant and fungal trees of life, investigate the evolution of morphological and ecological traits, and quantify and describe new taxa. We investigate how distributions of extant taxa have been shaped by evolutionary processes over geologic time. We generate genomic data to reconstruct phylogenies and conduct field- and herbarium- based study to understand trait evolution and to identify diagnostic features of taxa.
News
Contact
For enquiries, please email Dr Jo Birch - joanne.birch@unimelb.edu.au
Meet the Birch Lab group members.
Group members
Grace Boxshall
Luke Vaughan
Alexandra Sharples
Dr Jo Birch is also part of the Plant Systematics Research Group, working alongside academics Mike Bayly and Andrew Drinnan.
Alumni
Dr Bee Gunn
Declan Blackburn
Aiden Webb
Cody Hajnal
Grace Boxshall
Candice Farrugia-Roberts
Ongoing research projects in the Birch Lab: Plant and Fungi Systematics.
1. Asparagales
The Asparagales order contains one third of all monocots, spread across 14 families. The order includes species rich families such as the Orchidaceae and economically important species such as Onion, Agave, and Iris.
Australasia is the centre of diversity of non-Orchidaceae Asparagales and contains significant native diversity (48 genera, c. 327 spp), including the iconic grass-trees (Xanthorrhoea). Despite this species richness, understanding of Australasian Asparagales diversity is incomplete.
My students and I have research projects underway investigating the evolution of Australasian Asparagales.
Projects include work to:
- Reconstruct phylogenies for Australasian Asparagales genera (e.g. Astelia, Borya, Caesia, and Lomandra) to understand their relationships and to trace the evolution of their ecological and morphological diversity.
- Estimate the evolutionary signal in nuclear genomes: we reconstruct phylogenies based on nuclear (HybSeq, A353 bait) data to study the divergence of Australian taxa at deep and shallow time-scales.
- Investigate Austral Biogeography using plant and fungal lineages with centers of diversity in Australia and New Zealand to understand how distributions of extant taxa have been shaped by evolutionary processes over geologic time.
- Describe taxa and revise taxonomic circumscriptions. We use molecular and morphological data to test taxonomic hypotheses and revise generic and species circumscriptions.
2. Herbarium Digitisation and Machine Learning Technologies
Biodiversity data such as those that accompany museum and herbarium specimens comprise a massive global data resource. Digitising the data from specimens currently accessioned in the worlds museums and herbaria is a massive and labour-intensive undertaking. When these data are readily accessible they enable rapid biodiversity analyses and can inform conservation and policy decision making.
Current research investigates the application of computer vision technologies to efficiently and accurately mobilise specimen associated collection data. Collaborations are focusing on generation of tools to extract, digitise, curate, and share herbarium specimen-associated data and to enable curation of digitally extended specimens and their data. It is essential that these biodiversity data are mobilised as efficiently as possible to enable their application within sectors that rely on accurate biodiversity data e.g. biosecurity, agriculture, food production, and climate science.
3. Fungi
When it comes to fungal diversity, best estimates indicate that between 92%-95% of fungi have yet to be scientifically described. Current research in my lab, collaborating with mycologists at Australian herbaria, focuses on reconstructing phylogenies to understand the evolution of Ascomycota and Basidiomycota families that are species rich in Australia.
This research provides a phylogenetic context that informs species discovery, enables description of new species, and enables us to investigate how morphological and ecological traits, such as toxicity, truffle-like fruitbody form, and trophic guild, have evolved in these lineages. We generate data that increases knowledge of species distributions and, in conjunction with biogeographic analyses, enable investigations of how distributions of extant taxa have been shaped by evolutionary processes over geologic time."
Research Techniques
Technologies applied include: field- and herbarium-based study, Next-seq Illumina sequencing, HybSeq (A353 baits), Diversity Array Technology (DArT), Flow Cytometry, Scanning Electron Microscopy (SEM), Computer vision methods.
Research and Industry Collaborations
We work in close collaboration with other researchers and research programs from around the world, as well as our local industry partners. These include:
- Melbourne Data Analytics Platform
- Royal Botanic Gardens Victoria
- Landcare Research, New Zealand
- Royal Botanic Gardens New South Wales
- South Australian Botanic Gardens and Herbarium
- West Australian Herbarium
- Managers of Australasian Herbarium Collection
Publications by Dr J. Birch
Zuntini, A.R., Carruthers, T., Maurin, O. et. al. (including J.L. Birch), 2024. Phylogenomics and the rise of the angiosperms. Nature. (doi.org/10.1038/s41586-024-07324-0)
Webb, A.T., R.L. Barrett, J.L. Birch. (2023) Caesia walalbai AT.Webb, Birch & R.L.Barrett (Asphodelaceae subfam. Hemerocallidoideae), a new species from south-east Queensland. Telopea 26: 159-168.
Thompson, K., R. Turnbull, E. Fitzgerald, J.L. Birch. (2023) Identification of herbarium specimen sheet components from high-resolution images using deep learning. Ecology and Evolution 13 (8): e10395.
Thompson, K. and J.L. Birch. 2023. Mapping the Digitisation Workflow in a University Herbarium. Research Ideas and outcomes, 9: e106883.
Gunn, B.F, D.J. Murphy, N.G. Walsh, J.G. Conran, J.C. Pires, M. Crisp, L. Cook, T.D. Macfarlane, and J.L. Birch. 2023. Phylogenomic data resolve phylogenetic relationships of Australian mat-rushes, Lomandra (Asparagaceae: Lomandroideae). Botanical Journal of the Linnean Society (doi.org/10.1093/botlinnean/boad034).
Turnbull, R., J.L. Steenwyk, S.J. Mutch, P. Scholten, V.W. Salazar, J.L. Birch, and H. Verbruggen. Orthoflow: phylogenomic analysis and diagnostics with one command (in prep).
Turnbull, R., E. Fitzgerald, K. Thompson, J.L. Birch. HESPI: A pipeline for automatically detecting information from herbarium specimen sheets. (in prep. HESPI: github.com/rbturnbull/hespi)
Birch, J.L. and A. Kocyan, 2021. Molecular Phylogenetics and Evolution. Biogeography of the monocotyledon astelioid clade (Asparagales): a history of long-distance dispersal and diversification with emerging habitats.
McLay, T.G.B., J.L. Birch, B. Gunn et al., 2021. Applications in Plant Sciences, New targets acquired: Improving locus recovery from the Angiosperms353 probe set, doi: 10.1002/aps3.11420.
Boxshall, A.-G., T. Lebel, J.L. Birch, M. Symonds, D. Callahan, 2021. A field-based investigation of simple phenol variation in Australian Agaricus xanthodermus, Mycologia.
Gunn, B.F, D.J. Murphy, N.G.Walsh, J.G.Conran, J.C.Pires, T.D.Macfarlane, and J.L. Birch. Evolution of Lomandroideae Thorne & Reveal (Asparagaceae Jussieu): Multiple origins of polyploidy and biome occupancy in Australia, Molecular Phylogenetics and Evolution, 149, 106836.
Ranatunga D., P. Milne, Birch, J.L. (2018) Digitise This! Innovation in digitisation initiatives within Australasian herbaria. Biodiversity Information Science and Standards 2, e26077.
Jobson, P., J.L. Birch et al. (2018) Managers of Australasian Herbarium Collections (MAHC): A MARK of curation excellence. Biodiversity Information Science and Standards 2, e26283.
Birch, J.L., N.G. Walsh, D.J. Cantrill, G.D. Holmes, D.J. Murphy (2017). Testing efficacy of distance versus tree-based methods for DNA barcoding of grasses (Poaceae tribe Poeae) in Australia. PLOS One, doi: https://doi.org/10.1371/journal.pone.0186259.
Birch, J.L. (2015) A revision of infrageneric classification in Astelia Banks & Sol. ex R.Br. (Asteliaceae). PhytoKeys 52: 105-132. doi: 10.3897/phytokeys.52.4768.
Birch, J.L., F.B. Berwick (student), N.G. Walsh, D.J. Cantrill, D.J. Murphy (2014[2015]). Distribution of morphological diversity within widespread Australian species of Poa (Poaceae, tribe Poeae) and implications for taxonomy of the genus. (Invited) Australian Systematic Botany ABRS special issue 27: 333-354.
Birch, J.L., D.J. Cantrill, N.G. Walsh, D.J. Murphy. 2014. Phylogenetic investigation and divergence dating of Poa (Poaceae tribe Poeae in the Australasian Region. Botanical Journal of the Linnean Society:175: 523-552.
Birch, J.L., S.C. Keeley (2013). Dispersal pathways across the Pacific: The historical biogeography of Astelia s.l. (Asteliaceae, Asparagales). Journal of Biogeography 40: 1914-1927.
Birch, J.L., S.C. Keeley, and C.W. Morden. 2012. Molecular phylogeny and dating of Asteliaceae (Asparagales): Astelia s.l. evolution provides insight into the Oligocene history of New Zealand. Molecular Phylogenetics and Evolution 65: 102-115.
Birch, J. L. 2011. The systematics and historical biogeography of the Asteliaceae (Asparagales). Doctoral Dissertation, University of Hawaii at Manoa.
Birch, J.L. 2009. A comparative analysis of nineteenth century pharmacopoeias in the Southeastern United States: A case study based on the Gideon Lincecum Herbarium. Economic Botany 63(4):427-440.
Birch, J. L. 2004. The Gideon Lincecum Herbarium: A Floristic and Ethnobotanic Analysis. Master’s Thesis, University of Texas at Austin.
General articles/reports
Birch, J.L. and Simpson, M. 22/06/2022. “The challenge to discover our plant and fungi species”. Pursuit [accessed here].
Holland, D. and Birch, J.L., 24/10/2018. “The stories of Australia’s botanical biodiversity”. Pursuit [accessed here]
Herbarium resources
Project lead on the development of The University of Melbourne Herbarium Collection Online to enable public online access to MELU collections.