Australian Tropical Herbarium Research and Programs Theme 1 – Tropical Biodiversity Science

Theme 1 – Tropical Biodiversity Science

Species discovery, evolutionary biology, species/vegetation community mapping, with a focus on understudied groups, ecosystems and areas.

Phylogeny and systematics of ferns and lycophytes using next-generation high-throughput DNA sequencing / GoFlag project

Pteridophyta is the common name given to the phyla Lycopodiophyta and Monilophyta, the lycophytes and ferns. Their family and generic radiation has been interpreted in varying ways giving rise to unstable generic and species classification. This project employs a global collaborative community derived approach and phylogenetic analysis of globally sampled next generation molecular and morphological data sets to resolve the higher family, subfamily, generic and species classification of the pteridophytes. In addition, advances in global herbarium and literature databasing and imaging has increased availability of original materials. This project also undertakes a census of original materials of Australian ferns and lycophytes to resolve taxonomic and nomenclatural issues in advance of molecular revision.


Ashley Field (ATH), Eric Schuettpelz (Smithsonian NMNH, USA), Weston Testo (U. Vermont USA), Thais Elias Almeida (UFOPA, BR), Emily Sessa (U. Florida, USA).

Host specificity of fungal endophytes of tropical Australian rainforests

This project examines the diversity and co-evolutionary relationships of fungi that form mutualistic associations with mountain-top restricted plant taxa. The focus of the project is foliar fungal endophytes, the fungi that grow inside plants without causing symptoms. Fungal endophytes are known to contribute to plant, and therefore forest health, and are being used elsewhere as a measure of fungal diversity in forests. This study is the first to investigate tropical fungal endophytes in an Australian context and will specifically address elucidating their biodiversity and host specificity in the forests of the Wet Tropics. In addition, host specificity will also be investigated using infra-specific taxonomic units (haplotypes) of the host (species of Elaeocarpus), and across a biogeographic barrier (Black Mountain Corridor), both for the first time internationally. Impacts of drought of fungal community structure will also be investigated using the drought experiment at the Daintree Rainforest Observatory. Foliar endophytes from three species of plants each from control and droughted forest will be analysed to determine the nature of changes in the fungal community.


Kaylene Bransgrove (ATH/JCU PhD student), Sandra Abell (WTMA/ATH).

Investigating species diversity in the genus Phlegmariurus (Lycopodiaceae) using Next-generation DNA sequencing

Phlegmariurus is the largest genus in the lycophyte family Lycopodiaceae. It occurs in the tropics worldwide and its species diversity and enumeration is poorly understood owing to conservative, habitat-driven morphological adaptations, polyploidy and potentially reticulate evolutionary history. Investigations using Sanger sequencing and morphological analyses have hitherto been unable to resolve the species level phylogeny in several complexes, particularly in the diverse Asian-Oceanian Phlegmariurus phlegmaria group. This project advances on existing phylogenetic investigations by using high-throughput Next-generation DNA sequencing to build a larger dataset on a finer scale species sampling of Phlegmariurus from Oceania and around the world.


Ashley Field (ATH), Weston Testo (U. Vermont, USA), Lucie Bauret (Xishuangbanna, China), Benjamin Øllgaard (U. Aarhuss, Netherlands), Germinal Rouhan (P, France), Thais Elias Almeida (UFOPA, Brazil).

Origins of the northern Australian flora – role of the Sunda-Sahul floristic exchange

Understanding the origins and evolution of the tropical biota requires phylogenetic hypotheses for a diverse range of lineages. This project is gap-filling published molecular phylogenies of northern Australian plant groups with missing taxa, dating these phylogenies, and using them to generate general explanations about tempo and direction of evolution of the northern Australian and Malesian floras: what elements of the extant flora are derived from Gondwanan stock (relictual taxa) that have differentiated in situ, what are the invasive elements, and where (and when) have they come from?


Lizzy Joyce (ATH/JCU PhD student), Darren Crayn (ATH), Katharina Nargar (ATH), Lars Nauheimer (ATH), Joseph Holtum (JCU), Kevin Thiele (independent researcher), Caroline Pannell (retired), Maurizio Rossetto (Royal Botanic Gardens, Sydney), Craig Moritz (Centre for Biodiversity Analysis, ANU/CSIRO), Paul Oliver (Griffith University).

Phylogenetics, systematics and evolutionary dynamics of Elaeocarpaceae

Molecular phylogenetic and biogeographic work is clarifying the origins and patterns of diversification among lineages within Elaeocarpaceae (including Tremandraceae). Within the phylogenetic framework, we are analysing population-level genetic and morphological diversity in selected species in order to provide insights into taxon boundaries, comparative evolutionary responses and speciation mechanisms in dry-adapted shrubs and rainforest tree species.


Janet Gagul (ATH/JCU PhD student), Darren Crayn (ATH), Sook-Ngoh Phoon (independent researcher), Yumiko Baba (Auckland Museum, NZ), Lars Nauheimer (ATH), Maurizio Rossetto (Botanic Gardens Trust, Sydney), Mark Coode (Kew Gardens, UK), Andrew Rozefelds (Qld Museum, Brisbane).

Systematics of miscellaneous tropical flora and fungi

Staff at ATH are engaged in small taxonomic projects on a range of different Australian tropical plant groups. The most significant of these projects are outlined in brief below. These projects are all largely collections and field based. Molecular phylogenetic and population genetic study is undertaken as appropriate.

Systematics and biogeography of Garcinia

The genus Garcinia (mangosteens, family Clusiaceae) is common in tropical regions around the world. Species are used widely by Indigenous and modern cultures for fresh fruits, food flavourings, chewing sticks, herbal medicines, food supplements and building materials. Garcinia has also been the subject of much research into novel antioxidants and xanthones that may provide health benefits. The phylogenetic relationships and evolution of traits, such as those valuable to humans, is not well known, due to difficulties such as the availability of material, large numbers of species with highly diverse morphological characters, and nomenclatural confusion. Garcinia has not been recently revised taxonomically, so our understanding of species and generic concepts is also not well understood.


Rismita Sari (ATH/JCU PhD student), Sandra Abell (ATH/JCU), Darren Crayn (ATH), Natalie Dillon (DAFF), Paul Gadek (independent researcher)

Macrofungi of northeast Queensland

Fungi are one of the most diverse and species-rich groups of life yet are understudied worldwide, and especially in far north Queensland. This project aims to facilitate and expand mycological research and collections within this region. Organisation of the FNQ MycoBlitz in 2009 by the ATH coordinated by Sandra Abell has continued to encourage both national and international collaborators to perform their research in the WTWHA. Of particular note are the more than 1000 collections made by Professor Emeritus David Largent during annual field trips from 2009 through 2012. Collections of macrofungi, entomopathogenic fungi and plant pathogenic fungi made during the 2018 mycology workshops by Sapphire McMullan-Fisher, Frances Guard, Matthew Barrett and Nigel Fechner, will form the basis for ongoing taxonomic work.


Sandra Abell (ATH), Sapphire McMullan-Fisher (FungiMap), Frances Guard (QMS), Nigel Fechner (BRI), Matthew Barrett (ATH), Teresa Lebel (MEL), and various collaborators.

DNA-Barcoding of ectomycorrhizal hypogeous fungi

Hypogeous fungi are an incredibly diverse and polyphyletic group that have co-evolved with animals (that eat and disperse them) and plants (that form ectomycorrhizas). Despite their ecological importance they have been relatively understudied in the Australian tropics. This set of projects aims to generate and use DNA barcodes to identify and classify Hysterangiales species collected from the Australian tropics, and determine how the community of ectomycorrhizal fungi collected as hypogeous sporocarps relates to the functional (root-tips) ectomycorrhizal fungal community within the same habitat. This project will also identify the fungi found in the scats of a specialist mycophagous marsupial (Bettongia tropica) and those in the soil and plant root-tips to determine the importance of the bettong in providing dispersal of fungal spores as an ecosystem service. This project was supported by Caring for our Country in collaboration with the World Wildlife Fund (WWF), the Queensland Dept. Environment and Heritage Protection (EHP), and the Queensland Parks and Wildlife Service (QPWS). DNA barcoding of ectomycorrhizal hypogeous fungal species as well as next generation sequencing, bioinformatics and analysis of root-tip, soil and scat samples from the northern bettong and other mammals has been completed for this project. Two chapters from Nuske’s 2017 thesis have now been published and a third will be submitted in 2018. The systematics of Hysterangiales will be incorporated into the new project ‘Truffle-like fungi (Basidiomycetes): taxonomy, systematics and a revised classification for all Australian taxa’ funded by the ABRS 2017-2020 and administered by MEL. This project aims to conduct phylogenetic analyses for exemplars of all known Australian truffle-like genera, utilising existing and novel sequence data, to provide an updated classification of global application. This project will increase taxonomic and systematic knowledge of a poorly understood, cryptic group of fungi, and provide a unique opportunity for the transfer of taxonomic knowledge.


Sandra Abell (ATH/JCU), Susan Nuske (JCU PhD student), Teresa Lebel (MEL), Michael Castellano (Oregon State University).

Next-generation systematics: unravelling evolutionary relationships in Australasian orchids

Standard molecular markers provide only limited insights into phylogenetic relationships in cases where plant groups a) underwent recent and rapid diversification, b) are subject to reticulate evolution, and/or c) exhibit polyploidy. Next-generation sequencing technologies now offer the opportunity to investigate the evolution of such challenging plant groups. In this project we aim to apply next-generation approaches to unravel inter- and infrageneric relationships in taxonomically difficult Australasian orchid groups, such as the Thelymitrinae, Prasophyllinae and Caladeniinae, to re-assess their systematics.


Katharina Nargar (ATH), Lars Nauheimer (ATH), Natascha Wagner (U. Goettingen), A Atsawawawarunt (Imperial College London), Christian Laudereau (Herbarium Nouméa, New Caledonia), Allison Welsh (U. Wollongong), Kate O'Hara (CSIRO vacation scholar), James Perkins (CSIRO vacation scholar), Darren Crayn (ATH), Mark Clements (CANBR).

Regional Ecosystem Mapping

The Queensland Herbarium’s Regional Ecosystems (RE) Mapping Program is an extensive survey, mapping and monitoring program of the state. The RE maps, which show pre- clearing, remnant vegetation and regional ecosystems, are important tools for governments, landholders and scientists to plan and manage the natural environment, developments and vegetation restoration. As part of the RE mapping program, ATH staff are updating and refining (at 1:100,000 scale) the Cape York Peninsula and Einasleigh Uplands bioregions and the Wet Tropics bioregion mapping at 1:50,000 scale. This is extending to incorporating and updating the mapping and classification of wetlands and ground water dependant ecosystems.

A standardized numerical classification methodology for regional ecosystems has been developed and is being implemented. Work will commence on rolling this out to the non-rainforest Regional Ecosystems in the Wet Tropics bioregion. Collaborative work with CSIRO as part of a NESP project on pig eradication in the Archer River basin on Cape York will be completed. Staff from ATH will continue to advise and assist in the incorporation of this numerical classification methodology into other bioregions across the state. Incorporating and updating wetlands ground water dependent ecosystems in to the RE mapping down to 1 ha scale will continue in all three bioregions.


Eda Addicott (ATH), Peter Bannink (ATH), John Neldner (DES), Mark Newton (ATH).