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

​

Collaborators: James Clugston (lead), Lyn Cook, Michael Crisp, Peter Jobson, Brendan Lepschi, Matthew Renner and Peter Weston

​

Australia has a very diverse pea-flowered legume flora with 1,715 native and naturalised species currently recognised. Tribe Mirbelieae s.l. includes 44% of Australia’s peas in 24 genera with 756 recognised species. However, several genera within the Pultenaea alliance in tribe Mirbelieae are considered polyphyletic and two main options have been proposed: 1. Merge ca. 18 genera containing c. 540 species (the largest genus, Pultenaea has nomenclatural priority), or 2: Re-circumscribe some genera and describe new genera as required to form monophyletic groups. At the species level, option 1 would require 76% of names to be changed; whereas based on available data, option 2 is likely to require at most 8.3% of names to change. Option 2 therefore provides the least nomenclatural disruption, but cannot be implemented without a robust phylogenetic framework to define new generic limits. Novel analyses of available plastid DNA data (trnL-F) suggest that option 2 is feasible once sufficient data can be generated to resolve relationships. However, reticulate evolutionary histories or past rapid speciation suggested for this group may prevent the resolution of all nodes. We propose targeted use of Next-Generation Sequencing technology as the best way to resolve relationships between key clades in the tribe.

​

A new global classification for Cyperaceae including stabilisation of names to genus level in Australian sedges

​

Collaborators: Isabel Larridon (lead), Alexandre R. Zuntini, Étienne Léveillé-Bourret, Julian Starr, Muthama Muasya, Tamara Villaverde, Kenneth Bauters, Grace Brewer, Jeremy Bruhl, Suzana Costa, Tammy Elliott, Niroshini Epitawalage, Marcial Escudero, Isabel Fairlie, Paul Goetghebeur, Andrew Hipp, Pedro Jiménez-Mejías, Izai Sabino Kikuchi, Modesto Luceño, José Ignacio Márquez-Corro, Santiago Martín-Bravo, Olivier Maurin, Lisa Pokorny, Eric Roalson, Ilias Semmouri, David Simpson, Daniel Spalink, Wayt Thomas, Karen Wilson, Martin Xanthos, Félix Forest, and William Baker

 

Cyperaceae (sedges) are the third largest monocot family and are of considerable economic and ecological importance. Sedges represent an ideal model family to study evolutionary biology because of their species richness, global distribution, large discrepancies in lineage diversity, and broad range of ecological preferences. Goetghebeur’s seminal work on Cyperaceae published in 1998 provided the most recent complete classification at tribal and generic level, based on a morphological study of Cyperaceae inflorescence, spikelet, flower and embryo characters plus anatomical and other information. Over 20 years after the last comprehensive classification of the family, we present the first family-wide phylogenomic study of Cyperaceae based on targeted sequencing using the Angiosperms353 probe kit sampling 311 accessions. Informed by this backbone phylogeny, a new classification for the family at the tribal, subtribal and generic levels is proposed. We provide a taxonomic treatment including identification keys and diagnoses for the 2 subfamilies, 24 tribes and 10 subtribes and basic information on the 95 genera recognised. Recent publications relevant to Australian Cyperaceae include six new subtribes in tribe Schoeneae: Anthelepidinae, Caustiinae, Gymnoschoeninae, Lepidospermatinae, Oreobolinae and Tricostulariinae. Four new genera have been described in recent years, Ammothryon, Anthelepis, Netrostylis, and Scleroschoenus. The genus Chaetospora has been reinstated, Abildgaardia is supported as distinct, and Baumea, Crosslandia and Tetrariopsis are included under revised circumscriptions of Machaerina, Fimbristylis and Morelotia respectively. It is estimated that there are 240–360 new sedges species to be described in Australia.

​

Keys to the flora of the world renown Kimberley region of Western Australia and a bibliographic synopsis

​

This project will deliver an 800+ page publication providing identification keys to 3,500 vascular plant taxa in north-western Australia. It also includes representative colour photographs, comprehensive bibliographic data, misapplication of names, type citations and synoptic flowering and distribution data. Updating the Flora of the Kimberley Region (Wheeler 1992), which included 2,045 taxa, it includes many ‘phrase-name’ taxa for which there is currently no published identification tool. Nearly a quarter of a century in compilation, this will be an essential tool for identifying plants in north-western Australia. A summary of my work in the Kimberley can be read here. Funded by an Australian Biological Resources Study Bush Blitz grant.

 

Cryptic speciation in Arivela (Cleomaceae)

​

Collaborators: Margaret Byrne, David Coates, Craig Moritz, Kym Ottewell, Kevin Thiele

 

This project is investigating cryptic speciation in Australian species of Arivela (formerly included in the large genus Cleome; Cleomaceae). It complements phylogenomic studies for a recent ARC Linkage Grant “Phylogenomic assessment of conservation priorities in two biodiversity hotspots: The Pilbara and the Kimberley”. There appears to be a high level of cryptic speciation in several species complexes not identified in the existing Flora of Australia account. Most Australian native species are best placed in the segregate genus Arivela and new combinations have been made (Barrett et al. 2017). However, the unusual C4 species Cleome oxalidea, endemic to the tropical arid zone of Australia, was found to be an isolated lineage, described as a new genus Areocleome. Both molecular markers and morphological characters are being used to assess taxonomic limits in the genus. Funded by an Australian Biological Resources Study grant.

​

Small worlds – can micromorphology of seeds distinguish new species in the global genus Fimbristylis?

 

Collaborators: Jessie Knott, Sarah Mathews

 

Led by Jessie Knott as a Summer Student at CSIRO, Black Mountain (now studying education at the University of Melbourne) we used Scanning Electron Microscopy to create a comprehensive image library for Australian Fimbristylis species (in the sedge family, Cyperaceae). Using this image library, Jessie assessed character variation to understand species' relationships and identify putative new species with distinctive seed morphology. Funded by the CSIRO Summer Scholarship Program.

 

Species boundaries in Erythrophleum (Fabaceae: Caesalpinioideae) in Australia

 

Collaborator: Matt Barrett

​

A small genus of about 10 species distributed across Africa to South-east Asia and Australia. Fieldwork in northern Australia has shown that three species should be recognised in Australia. Found from the Great Sandy Desert in Western Australia, to the tip of Cape York in Queensland, this genus occurs in a wide range of habitats. It has many traditional uses and is an important native timber source in the Northern Territory as it is one of the few species resistant to termites. The core wood is deep red in colour, and very hard, making it excellent for woodworking. On a note of caution, almost all parts of the plant are highly toxic to both people and livestock, and even dust from cut wood can be highly irritating.

 

Phylogenetics of the Sword sedges (Lepidosperma) and allied genera

 

Collaborators: Matt Barrett, Jeremy Bruhl, George Plunkett, Mark Wallace, Karen Wilson

 

One of Australia's largest genera, Lepidosperma is a common component of many ecosystems in southern and eastern Australia (Barrett & Wilson 2012; Barrett 2013). With a few species extending to New Zealand, New Caledonia, New Guinea, Borneo, Malaysia and China, it presents many exciting opportunities to study patterns of biogeography and speciation. With large numbers of undescribed species, the species-level taxonomy of this genus only now being determined. It is estimated that over 200 species are yet to be formally named, most of these from Western Australia. New species are also known from most Australian states.

 

Seed micromorphology and speciation in the Australian–New Zealand genus Poranthera (Phyllanthaceae)

 

Poranthera is a small genus of tiny annual herbs or small herbaceous perennials found in Australian and New Zealand. 15 species were recognised in the most recent revision of the genus. I have since described two additional species from Western Australia (Barrett 2014; Barrett & Barrett 2015). My current studies are focused on seed micromorphology across the genus, using Scanning Electron Microscopy (SEM). I am particularly investigating the P. microphylla species complex, which clearly includes multiple species in its current circumscription. This species has the widest distribution of any in the genus, currently spanning from south-west Western Australia to the east coast, to the Queensland tropics, and west to the Kimberley on the Australian mainland, also occurring in Tasmania and New Zealand.

 

Seeds of truth? Utilising Scanning Electron Microscopy to assess patterns of Carnivore evolution: a global survey of seed morphology in the genus Drosera (Droseraceae)

 

Collaborator: Allen Lowrie (note Allen sadly passed away in August 2021)

 

Carnivorous plants, and Drosera in particular, are a fascinating group with a near-global distribution, but a high centre of diversity in Australia. Seed morphology in the genus is remarkably variable, yet detailed comparative studies have not previously been undertaken. We have imaged seeds of almost all known Drosera species. The seed morphology of each species is being described in detail and these characters are being assessed against existing classifications and phylogenetic data to test for key morphological traits associated with the evolution of this diverse genus.

​