AVH welcomes new data provider: the University of Melbourne Herbarium (MELU)

This week, Australia’s Virtual Herbarium (AVH) welcomed a new data provider: the University of Melbourne Herbarium (MELU). Home to approximately 100,000 specimens, MELU is the largest university herbarium in Australia. About 10 per cent of the collection has been databased to date, adding over 9,000 records to AVH.

The MELU herbarium was established in the School of Botany in 1926 with a donation of plant specimens from the Rev. Herman Montague Rucker Rupp, a former student of Trinity College at the University. The collection grew throughout the 20th century thanks to donations from state and private herbaria, and through the efforts of staff and students in the School of Botany.

Herbarium cabinets at MELU

The original herbarium cupboards that were built to house Rupp’s collection are still used today. They have moved buildings twice and are now used in conjunction with rolling compactus to house the c. 100,000 MELU specimens.

Although small in size compared to the state and territory herbaria, it is the largest and most botanically diverse university herbarium, and makes a valuable contribution to our combined knowledge of the Australian flora. All major botanical groups are housed in the collection, but it is particularly rich in algae and non-vascular plants. Significant collections include:

  • An algae collection of approximately 30,000 specimens, which was established by the renowned phycologist, Dr Sophie Ducker. MELU volunteers have recently databased some of Ducker’s collections from Madagascar and the Mascarene Islands.
  • 4,500 mosses and liverworts collected by George Scott, the foremost authority on temperate mosses and liverworts. Scott is credited with rekindling interest in the study of bryophytes in southern Australia and was the teacher of at least three of today’s leading Australian bryologists. MELU have recently begun databasing the Scott collection, which is available in AVH alongside records of Scott specimens held in other herbaria.
  • A collection of leaf-inhabiting microfungi specimens, slides and illustrations from Dr Harry Swart, a mycologist, plant pathologist, and artist of architectural and humorous drawings. Swart joined the School of Botany in 1966 as a Senior Lecturer. Leaf-inhabiting fungi are a highly diverse but relatively unexplored group of fungi that are prevalent on many of the iconic Australian plant genera such as Eucalyptus and Banksia.

More MELU specimen records will be added to AVH as the collection continues to be databased by a team of volunteers – who are mostly undergraduate students – and herbarium staff. Volunteering at the herbarium gives students great insights into botanical diversity as well as an understanding of how natural history collections are managed.

“Students get to see a range of different plants, which gives them a good idea of morphological variation and spotting characteristics, while helping us curate the collection”, says Herbarium Curator, Dr Gillian Brown.

Although all herbaria are important research collections, university herbaria, in particular, have an important role in teaching the next generation of botanists. The herbarium is a valuable teaching resource, explains Brown.

“Specimens are used in practical classes to demonstrate the diagnostic features of different plant groups and some subjects require students to prepare their own specimens, which in turn are incorporated into the collection.”

One of the most important teaching and research collections is a collection of approximately 7,000 Eucalyptus specimens collected by staff (including Professors David Ashton and Pauline Ladiges) and students over the years. The most significant of these is the monocalypt collection – Eucalyptus subgenus Eucalyptus – which comprises about 2,600 specimens from western and eastern Australia. This collection encompasses all species of the subgenus and includes voucher specimens sampled for DNA sequencing, seedlings cultivated from the specimens (which display characters useful for identification) and collections preserved in alcohol for microscopy. Multiple samples from different populations exist for many species, illustrating their geographic and morphological variation.

There are 16 herbaria in Australian universities, which together house over 420,000 specimens. MELU is only the second university herbarium to join AVH. The N.C.W. Beadle Herbarium (NE) at the University of New England joined AVH in 2013, and has over 80,000 records in AVH. Several other university herbaria are working towards delivering data to AVH, and we hope to have the La Trobe University Herbarium (LTB) and James Cook University Herbarium (JCT) on board in the coming months.

Tetratheca ciliata specimen

Curator Dr Gillian Brown’s favourite specimen: Tetratheca ciliata (MELU D015072a)

Rhodocallis elegans specimen

Rhodocallis elegans (MELU A110065a), a red algal specimen collected in Warrnambool, Victoria by Prof. Gerry Kraft in 1995

Herbarium volunteer working with the fungi collection

Herbarium volunteer Megan Rixon curating the fungal collection at MELU. Megan has databased over 200 specimens of fungi.

Isotype of Eucalyptus verrucata

Isotype of Eucalyptus verrucata collected from Mount Abrupt, Grampians Victoria, October 1979 by then student Julie Marginson.

Eucalyptus globulus specimen

A Eucalyptus globulus specimen (MELU D103755a) collected by Ian Clarke in 1977 on the University campus. This is one of thousands of high-resolution images of eucalypt specimens at MELU.

Australia’s Virtual Herbarium: 5 million records and counting

PRESS RELEASE, 12/08/2014

An Australian online resource, which is proving invaluable for scientific research and conservation efforts here and overseas, reached a significant milestone this week.

Australia’s Virtual Herbarium (AVH, http://avh.chah.org.au/) – one of the world’s largest repositories of specimen-based botanical information – now contains over 5 million records.

“This milestone represents a mammoth collaborative effort from Australian herbaria, who have worked together for over 25 years to make the information associated with herbarium specimens easy to share and reuse by anyone, anywhere in the world”, said Kevin Thiele, Chair of the Council of Heads of Australasian Herbaria.

AVH brings together specimen data from many of Australia’s herbaria – specialised museums that house collections of dried plants, algae and fungi – and makes it freely available on the web, providing the most complete and up-to-date picture of Australia’s botanical diversity available. Combining these data sets and providing easy access to them expedites research and allows scientists to undertake large-scale research projects previously not possible.

AVH is delivered through the extensive infrastructure provided by the Atlas of Living Australia (ALA, http://ala.org.au/). Through the ALA, AVH data is linked to a large and growing number of environmental data sets, facilitating research that leads to a deeper understanding of Australia’s biodiversity.

AVH makes Australia uniquely placed to be a testing ground for new research methods. Recent research by Brent Mishler, a biology professor at the University of California, Berkeley, and colleagues at the Centre for Australian National Biodiversity Research in Canberra, used AVH data to develop and test methods for identifying areas of high genetic diversity, which may be in need of greater conservation protection.

“Australia presents the best current opportunity for studying large-scale patterns of diversity because of the nearly complete digitisation of herbarium collections by Australia’s Virtual Herbarium. These new landscape-scale methods are not feasible in the US until we have more herbarium data available”, said Mishler.

Using Australian acacias as an example, their research identified biologically important, but currently unprotected, areas in Western Australia and confirmed the significance of the world heritage listed Wet Tropics of Far North Queensland. “We now have a richer view of biodiversity that takes into account the number of species, their rarity in the landscape and the rarity of their close relatives”, Mishler said.

AVH data has also been applied to conservation efforts in other parts of the world. Researchers in South Africa have used herbarium specimen data to model the distribution of potentially weedy Australian species – including eucalypts, casuarinas and acacias – outside Australia and predict the likelihood that they will become invasive. “AVH data has been absolutely crucial for much of this work”, said David Richardson, Director of the Centre for Invasion Biology at Stellenbosch University.

The combined collections of Australian herbaria are estimated to exceed 7 million specimens and are expanding all the time. “Our herbaria are active research collections that are always growing. They contain specimens from the earliest European explorations of Australia to the most recent botanical expeditions. New specimens are added daily as botanists continue to investigate our native and naturalised flora”, said Thiele. This ongoing collecting and databasing makes AVH the most up-to-date reference data set for Australian botanical diversity.

The ALA is a partnership of Australian herbaria, museums, CSIRO, government agencies and other biological collections. The ALA is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy (NCRIS) and the Education Investment Fund (EIF) Super Science initiative.

Further information

Kevin Thiele

Chair, Council of Heads of Australasian Herbaria

kevin(dot)thiele(at)dec(dot)wa(dot)gov(dot)au

Fiona Brown

Communications Advisor, Atlas of Living Australia

fiona(dot)brown(at)csiro(dot)au

 

Australian acacias

Using AVH data on Australia’s acacias, researchers have identified areas of high genetic diversity where improved conservation efforts might preserve rare and endangered species. Image: Andrew Thornhill.

AVH map

AVH map showing the distribution of the fungus Banksiamyces (red dots) and its host Banksia (blue dots), based on label data from specimens held in Australian herbaria. Image: Australia’s Virtual Herbarium (2014).

Banksiamyces macrocarpus

Banksiamyces macrocarpus, growing on cones of the Hairpin Banksia, Banksia spinulosa. Image: Geoff Lay CC BY-SA 3.0.

Banksia serrata

A herbarium specimen from which information has been digitised and made available in AVH for people to access anywhere in the world. This specimen of Banksia serrata, collected by Joseph Banks and Daniel Solander at Botany Bay in 1770, is held at the National Herbarium of Victoria at the Royal Botanic Gardens Melbourne. Image: Royal Botanic Gardens Melbourne.

Research links

Further information on the research by Mishler and colleagues is available at the Berkeley News Center: http://newscenter.berkeley.edu/2014/07/18/big-data-guides-conservation-efforts/, and the published research is available on the Nature Communications website: http://www.nature.com/ncomms/2014/140718/ncomms5473/full/ncomms5473.html.

David Richardson’s work is described in the journal Diversity and Distributions: http://onlinelibrary.wiley.com/doi/10.1111/j.1472-4642.2011.00824.x/abstract.

Other examples of research utilising AVH can be provided on request.

AVH data contributes to research on crop wild relatives

In February 2011, the International Centre for Tropical Agriculture (CIAT) in Colombia accessed data from Australia’s Virtual Herbarium (AVH) for use within the ‘Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives’ project, which is led by the Global Crop Diversity Trust in partnership with the Millennium Seed Bank, Royal Botanic Gardens, Kew. More information on the project can be found here.

Between 2011 and 2013, CIAT and project partners have been collating, processing and using occurrence data from numerous sources around the world to model the distributions of the wild relatives of major crops and to identify gaps in their conservation, using methods based upon those described here. A full list of the data providers is presented here.

The researchers gathered and processed 5 million occurrence records, including over 100,000 herbarium records from AVH, and are nearing completion of ‘gap analysis’ work for the 29 crop genepools. Gap analyses for the wild relatives of an additional 60 important crops will be completed in 2013; the results of the analyses will be made freely available on the project website. The interactive map for displaying the gap analysis results will be launched mid-year.

In addition to the results, the full data set will also be made available for use by other researchers under the Creative Commons License (Non-commercial, Share-alike, 3.0 Unported).

As a service to the data providers of the project, the researchers returned occurrence data to the original providers, with feedback on suspected errors in taxonomic and geographical data. AVH data custodians have started checking through this data, and will update their records where additional data was provided or genuine errors were detected.

New release of AVH

Dear AVH user,

The Council of Heads of Australasian Herbaria (CHAH) is pleased to announce the release this week of a new version of Australia’s Virtual Herbarium (AVH). The new site was developed by, and forms part of, the Atlas of Living Australia (ALA).

The URL for the new site is avh.ala.org.au. We have redirected the old site to this address; please update your bookmarks accordingly.

This version of AVH contains several key improvements, including:

  • extended query functionality
  • improved taxon name resolution: search results for taxon names will include synonyms
  • improved mapping capability and better options for downloading maps
  • e-mail alerts when records of interest to you are added, updated or annotated
  • the ability for users to flag potential data issues for individual records.

Please note that no registration or login is needed to access or download data from AVH. All data, except for records of certain taxa that are sensitive for conservation or biosecurity reasons, are accessible to everyone. We do, however, encourage regular AVH users to register with the ALA, as registration makes some extra features available. See the Help page for more information on registration and the benefits it brings.

This latest version of AVH represents an important step in unlocking the wealth of botanical information held by Australian herbaria and making it more easily available to the public. We trust you will find it a great improvement on the previous version of AVH.

The new AVH will be officially launched later this year. In the meantime, the AVH and ALA teams are still adding content and working to fix some minor bugs. We encourage users to provide feedback on how the site could be improved via the ‘AVH feedback’ link at the bottom of each page, or at avh@ala.org.au. If you need help with using the site, please consult the Help and AVH data pages.

I would like to acknowledge the enormous amount of work that has gone into developing, testing and documenting this new version of AVH, both from members of the ALA development and management teams, and from members of CHAH’s Herbarium Information Systems Committee (HISCOM). I would particularly like to thank Dave Martin and Nick dos Remedios from the ALA, and Niels Klazenga, Ben Richardson, Alison Vaughan and Aaron Wilton from HISCOM for shouldering the bulk of the work and producing what I hope you agree is a brilliant new AVH.

Regards,

Kevin Thiele
Chair, Council of Heads of Australasian Herbaria.