australia - · pdf fileschool of animal biology, the university of western australia, 35...

63

Upload: dinhtuong

Post on 28-Mar-2018

224 views

Category:

Documents


7 download

TRANSCRIPT

Page 1: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4
Page 2: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4
Page 3: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4
Page 4: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4
Page 5: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4
Page 6: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4
Page 7: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4
Page 8: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4
Page 9: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4
Page 10: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4
Page 11: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Western Australia has the longest historical record of biodiversity exploration and biodiversity data in

Australia, dating at least to Vlamingh’s and Dampier’s visits and biodiversity collecting in the Swan River and

Shark Bay in the late 1600s. This talk will provide a historical overview of biodiversity data and informatics in

the largest state in Australia, and discuss significant achievements and issues, with a particular focus on plant

data. An enormous amount of biodiversity data has been collected in WA over 300 years, from the earliest

specimens during the phase of European exploration, through active government and citizen science projects

in the 20th Century, to significant industry investment particularly during the years of the resource boom, and

continuing. While much has been achieved, many challenges remaining in making the best use of, and

mobilising, these data in the service of research, development and conservation.

Page 12: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

WA is a big and a marvellous place! Facing the Indian Ocean, it boasts the longest coastline of any

state and almost 1/3 of Australia’s maritime exclusive economic zone. Its marine environment

extends from the tropical north to the cool temperate south and these waters support a high

diversity of marine habitats and organisms, including numerous unique species. Two of Australia’s

four marine-based World Heritage areas and two of five bioregions are off our coast. WA is also

home to eight of Australia’s 15 biodiversity hotspots. But compared to many other marine

environments, scientific exploration of WA’s marine environment has been limited as our coastline

has only been subjected to European settlement and industrialisation for approximately 200 years.

However, over the past decades, WA has experienced one of the most significant and protracted

periods of private capital investment in its history. Investment in the expansion of existing, and the

development of new, resource projects (primarily iron and offshore oil and gas) is resulting in

massive off-shore infrastructure expansion, the development of new ports and increased vessel

movements, as well as fuelling unprecedented population growth.

The State’s biodiversity is an important asset that must be carefully managed and protected for

future generations. A deeper understanding of the natural environment will mitigate the impact of

human activity, create knowledge that can be harnessed to pursue bio-technological advances and

assist in the protection and conservation of WA habitats. In the absence of sound scientific

knowledge, poor understanding of the WA marine environment poses risks, such as irreparable

environmental damage caused by ill-informed decisions.

Western Australia has a significant biodiversity research base in marine science and is fortunate to

have substantial public capability. The State Government plays a major role in managing the

State’s biodiversity and its conservation, environment and collection agencies have considerable

expert science capabilities. Commonwealth, State, industry, businesses, academic organisations

and research institutions at the local level and worldwide are also working together to deliver

large-scale marine research in multi-disciplinary and holistic ways, to address key ocean

challenges.

With the enormous research effort occurring in WA, significant activities and growing

collaboration within WA’s data sector are being planned, or are currently underway, that have the

potential to establish WA as a world leader in data science innovation and expertise. The State

Government is supporting the growth of WA’s data sector through investment in radio astronomy,

supercomputing and data linkage. Supercomputing is the key to capitalising on the opportunities

offered through data intensive science. The Pawsey Centre’s processing and storage capacity will

support the State’s future computing requirements across each of the State Government’s five

science priorities. The Pawsey Centre also offers training in bioinformatics, scientific computing

skills providing opportunities to access careers in research and ICT in WA. Is this an opportunity for

the ALA to exploit?

Page 13: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Aggregated biological data that is widely and freely available provides an invaluable resource to

underpin the conservation of biological diversity. These data can be used directly by land managers,

or by scientific researchers with the aim of informing land management decisions. While many

biodiversity aggregation databases are great at capturing the distribution of native collection

records, strong biases exist against non-native records. This, in part, relates to the type of data

curated and the biases of collectors, as well as the common rationales underpinning non-native

observation data. Given that non-native weeds represent one of the greatest threats to terrestrial

biodiversity, there are many reasons why we should be looking to improve our knowledge about

just where is weedy in Australia. Here we explore the historical context behind the current

availability of non-native plant data and what it means for end users of that data. We outline our

findings from a pilot study in the Pilbara where we showcase how aggregating disparate data on

non-native plants can provide unique insight to help land managers prioritise funding for weed

control. Lastly, we highlight how emerging changes in data collection and aggregation approaches

may provide a significant improvement on what is currently available.

Bruce leads the Ecosystem Change Ecology Team based in Perth, Western Australia. This multidisciplinary team generates knowledge on the mechanistic links and synergistic interactions between landscape change, species invasions and native species decline in terrestrial ecosystems. Bruce leads research and develops theory to underpin more effective policy and management actions for conservation, invasion and production challenges in the face of rapid global change.

1 CSIRO Land & Water and CSIRO Health & Biosecurity, Private Bag 5, P.O. Wembley, WA 6913, Australia 2 School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia 3 School of Animal Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia 4 Western Australia Department of Parks & Wildlife, Dick Perry Ave, Kensington, WA 6151, Australia

Page 14: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Since their foundation, the seven Western Australian Regional Natural Resource

Management (NRM) Groups have placed high value on the use and further development of

biodiversity information in their planning, programming and on-ground implementation.

Equally, they have placed high value in avoidance of duplication, and in collaboration with

existing agencies and institutions that can be both the source and destination for biodiversity

data. This collaborative approach has resulted in hundreds of field projects incorporating and

enriching extensive and rigorous biodiversity data – aimed at better knowledge, better

understanding, and better conservation outcomes.

Page 15: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

The delivery of specimen data via the internet has revolutionised the effectiveness of targeted flora

surveys for commercial projects in Western Australia. Queries on the known flora of a region and

the Australia-wide distributions of taxa can be discerned with a few key strokes, giving confidence

to consultants in the range of species that may encountered in a region and assisting with tentative

identifications of unfamiliar taxa made in the field. The available data can also hint at likely

taxonomic anomalies and potential occurrence of new species and help resolve such issues. Geoff

will highlight how his organisation uses the Atlas of Living Australia in targeted surveys and outline

a wish list that could help improve the experience for the Environmental Consultancy Industry.

Page 16: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Western Australia has a long history of volunteerism and citizen science with some recent

milestones reached. Citizen Science project data contribution from WA to the ALA is reviewed

and some suggestions for standard procedures to ensure citizen science data is well-formed,

well-housed and retrievable into the future.

p +61 8 9227 7309

e [email protected]

Page 17: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Over a relatively short period, the Atlas of Living Australia (ALA) has matured to provide the most

comprehensive repository available of Australian biodiversity data, and arguably the world’s most

capable online portal for querying, visualising and downloading biodiversity data. However, the

ALA creates no data – it sources its information from a wide variety of data-rich organisations,

some of which already have mature portals, resulting in multiple portals publishing the same data,

notable differences in detail, and occasional confusion as to the most appropriate portal to use.

From its initial inception the ALA’s goal has been to complement existing biodiversity systems.

Nevertheless, some organisations may question the business sense of maintaining their local

portals in a challenging funding environment while the ALA is offering such exceptional capability.

However, there are good reasons for organisations to maintain their existing investment. While

ALA and State portals may superficially appear to duplicate functions, the drivers for State-based

portals, particularly those with a regulatory or planning function, are different to the citizen

science and collections focus of the ALA, resulting in different approaches to data and users. An

ecosystem of complementary portals provides better conservation outcomes than one-size-fits-all.

This talk will discuss some of the comparative strengths of each portal and present guidelines to

assist users in determining the most useful portal in situations such as environmental impact

assessment, conservation planning and scientific research.

Page 18: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Collections of globally important species of high conservation value are held by the Western

Australian Museum Department of Aquatic Zoology (AZ). The data associated with these specimens,

colloquially referred to as TCLE taxa (Threatened, Critical, Listed or Endangered), from groups such

as giant clams, corals and sea cucumbers, hold important records of distribution in space and time.

These historical records are critical for conservation managers to consider in attempts to monitor,

assess, and potentially rehabilitate populations of threatened taxa in Australia. In 2014, WAM was

awarded a grant from the Atlas of Living Australia (ALA) to database and mobilize taxa with high

conservation profiles in the WAM AZ collections. This mobilisation or ‘unlocking’ of WAM collection

data to the ALA website will place important historical collection information into the hands of

conservation managers and others for improved decision making. A total of 1257 specimens newly

registered and 113 previously registered specimens with updated names have been added to WAM

database and uploaded to ALA.

Page 19: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Genetic data are maintained and made available to researchers by databases such as Genbank.

These data are frequently accessed by researchers to supplement their own data, and are a

fundamental part of accessing difficult to sample organisms and placing research into broader

contexts. However, these data are not easily linked to the collections where the specimens were

sourced. As such, errors in species identifications, higher systematic levels and genetic data

themselves can propagate in the published literature, create confusion, and impede decision

making for managers. Here we discuss these difficulties and identify how the Atlas of Living

Australia could play a role in integrating collections and genetic data, making research more

efficient and more resilient to taxonomic change.

Page 20: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

The vastly increased rates of discovery of new animal species in Australia – principally

invertebrates – is being led by more focused field work in more remote parts of the country, in

combination with molecular sequence data. The rate of discovery currently outstrips the

taxonomic community’s ability to name each new species (and new genera) in a timely fashion,

leading to shortfalls in communicating the results of these discoveries to external organisations

and interested parties. Staff in the Arachnology section of the Western Australian Museum

devised an alphanumeric code system based on three unique letters of the taxonomic group (e.g.

MYG for Mygalomorphae; DIP for Diplopoda) and three integers, assigned in a sequential fashion.

Each putative new species is assigned a unique code (e.g. MYG004) and assigned to a genus name

(e.g. Aname MYG004). Each code-based name is based on a registered museum specimen that

acts as the voucher specimen. Putative new genera are given similar codes, but are based on

letters, e.g. MYGAAA. We have effectively used this system for both morphological and sequence

based hypotheses of “distinctiveness” where it has been widely adopted by industry and

government, including nominations for threatened species. There appears to be little impediment

to rolling out a national scheme for all animal taxa, but it will rely on the cooperation of

systematists and museums. These species codes will then be sufficiently robust to enable their

inclusion in the Atlas of Living Australia.

Page 21: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Abstract

Annotations in the Atlas of Living Australia have so much potential, some of it unrealised. One

significant resource-saving for the collections community would be for the specimen database

environments to make full use of ALA's annotations API.

Page 22: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

The National Research Collections Australia is a relatively new entity charged with the care and

management of CSIRO’s biological collections.

Mobilising the data across collections so that they can be readily used for research is a key

element to achieving this mission.

Over the last 12 months the National Research Collections Australia (NRCA) has been working

on a Digital Strategy that will inform CSIRO on how it will progress the digitisation of the range

of specimen within the collections. This is from contextual data to images and genomes.

As a first step, NRCA has recently finished a pilot for a new Collections Management

System. How will this new system, in light of a broader digital strategy, play out in a possible

systems architecture that sees ALA as the core presentation and visualisation mechanism for

specimen data? It must allow interfacing with other environmental data sets and in the long

term be future ready for a digital research environment.

Page 23: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Ongoing recording, collation and aggregation of new biodiversity data from the field is critical to

continuous monitoring, analysis and management of changes in the distribution and status of

species populations. And not just species occurrence data, but also the context around an

occurrence point such as its location, environmental and species association context, the event

context, methods, etc. The large volumes of data required to effectively monitor over time demands

continuous contributions from all areas of society that work with or have an interest in biodiversity.

There are several tools already available to support data collection, but very few can claim to be

standards-based and even fewer which effectively enable data aggregation. Many are satisfactory

for the local needs for which they were developed, but can’t be easily accessed or used by other

communities without considerable modification or customisation, and very few of them share data

outside of themselves, let alone have the ability to do this machine-to-machine. In addition, many

communities are time and technically challenged, lacking the resources and/or knowhow to develop

and manage appropriate databases for the data which they collect.

BioCollect (http://www.ala.org.au/biocollect/) has been developed by the ALA to support

communities, researchers, ecologists, indeed anyone who is undertaking citizen science,

biodiversity and ecological surveys, or environmental intervention works projects. It is a cloud-

hosted data collection system with Facebook-like simplicity, yet powerful and flexible configurability

to enable people to collect everything from simple single species observations to complex method

and plot-based multi-species/attribute surveys, and even schedule-based activities in

environmental works projects. Species are recognised in the data and standards compliant

occurrence records are created automatically. These can then be harvested via web services directly

into aggregation databases such as the ALA or state databases. BioCollect is also mobile enabled.

Page 24: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Phylodiversity measures summarise the phylogenetic diversity patterns of groups of organisms. By

using branches of the tree of life, rather than its tips (e.g., species), these measures provide a

more detailed understanding of Australia’s unique biodiversity. Considering phylodiversity

measures in policy and program decisions provides an additional line of evidence, complementing

traditional prioritisation metrics such as species richness and weighted endemism.

As a biodiverse nation with a strong legislative and policy framework, there are many

opportunities to use phylogenetic information. In the Department of the Environment,

phylogenetic information has application to help assess grant applications, list threatened species,

input into recovery plans, identify priority areas for intervention with multiple outcomes, and

contribute to assessing impacts of development.

Page 25: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

We examined regional patterns of plant biodiversity across South Australia using large species

occurrence datasets from field plots and herbarium records, 727,417 records in total. Species

richness is commonly used to rate regional biodiversity but does not highlight uniqueness.

Endemism metrics based on the 'sum of inverse range-sizes' (SIR) combine richness with

uniqueness by down-weighting species (or phylogenetic branches) if they are widespread.

However, the method of range-estimation influences the result: estimates based on the number

of occupied map grid cells (frequency or area of occupancy) are weakly correlated with estimates

based on extent of occurrence, and highlight a different aspect of range-rarity. We mapped

species and phylogenetic endemism with range-size estimated by distance across the range, and

compared this to richness of categorically assigned South Australian endemics. These metrics are

additive because each species present in a sampling unit adds (or potentially adds) to the total

score. For this reason it is useful to test whether endemism is higher than expected, given species

richness, for example using non-parametric statistics. Identified centres of endemism differed

somewhat between range-based SIR methods and counts of categorical endemics, suggesting

contrasting emphasis and biases. Some locations in South Australia with unique plant biodiversity

were already recognised by experts. The hallmark of this study was the use of numerical and

repeatable methods and metrics highlighting different aspects of range-restriction and

conservation importance.

_______________________________________________ 1 The University of Adelaide 2 Department of Environment, Water and Natural Resources, South Australia

Page 26: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Conservation planning informed by evolutionary diversity aims to identify conservation options

which would minimise losses of diversity from the Tree of Life, recognizing that some species

represent a larger part of that diversity than others.

We present initial results of a conservation analysis of the Kimberley in north-west Australia. We

use systematic conservation methods to identify areas to best represent the phylogenetic diversity

of the region’s lizards, based on phylogeography of ten genera of geckoes and skinks.

This study illustrates important advantages of a phylogenetic approach to conservation. It

accounts for the ancestral relationships between biota in its measure of biodiversity. Perhaps

more importantly, it allows conservation to integrate diversity within and between species in its

priorities, effectively bypassing formal taxonomy. Conservation planning can thus be applied in

cases where taxonomy is incomplete, or aligns poorly to known diversity.

Page 27: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

For many, natural science collections conjure up images of a collection of dead things in jars, hidden

in a basement somewhere gathering dust. The reality could not be further from the truth.

Collections are a constantly evolving home to exciting and innovative science. Right now, the next

generation sequencing revolution is unlocking an unprecedented scale of evolutionary information

from not only traditional sources such as cryofrozen tissue, but from skin and bones and more.

Genomic data can now be extracted from extinct species groups and can considerably increase the

spatial and temporal coverage of some extant species. My talk will focus on using the Atlas of Living

Australia to optimise sampling strategy from museum collections. Destructively sub-sampling

museum specimens is not at trivial matter and therefore sampling design should be optimised to

ensure you get the right data for the least impact.

Page 28: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Digital collections provide an invaluable asset of spatial and taxonomic information for studies in

evolution, biogeography, phylogenetics, ecology and related areas. We developed a worldwide

database for 336 marsupial species in the world with a total of 449,983 spatial records that were

cleaned and mapped to identify and corroborate the species distribution range. The second

component of this study was a multi-gen phylogeny with 282 taxa with the major clades for

continents such as Americas, Australasia and south-east Asia. Our results showed that the

Americas are the place of origin for Australian marsupials. The microbiotheria group seems to

have dispersed from the Americas to Australia via Antarctica. The extant species Dromiciops

gliroides is the sister group of the Australian marsupials and they have been diversifying in the last

50 million years. The data available in the Atlas of Living Australia was an essential component to

build our database for my ongoing PhD project.

1. University of Canberra, Faculty of Applied Science, Institute for Applied Ecology, ACT 2601 Canberra, Australia2. Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Basin Futures, University of

Canberra, Australia.3. Queensland University of Technology, Science and Engineering Faculty. Earth, Environmental and Biological

Sciences, Bioscience . 2 George St, Brisbane QLD 4000. Brisbane, Australia.4. Centre for Australian National Biodiversity Research, Commonwealth Scientific and Industrial Research

Organisation, Plant Industry, Canberra, Australian Capital Territory, Australia, Australian Tropical Herbarium, JamesCook University, Cairns, Queensland, Australia

5. Australian Museum. 6 College St., Sydney NSW 2010.

Page 29: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Phylolink provides an online capability to integrate environmental, species distribution and

trait data with phylogenies. This provides an evolutionary view of biodiversity data and

supports studies in spatial phylogenetics, phylogenetic-based biodiversity assessments and

comparative biology. As a web-based tool, Phylolink uses web-services to access rich

collections of biodiversity data from many sources and integrate these onto a phylogenetic

tree. User-friendly interfaces and data sources make the tool readily accessible to new users

of phylogenetic approaches, while a high degree of flexibility and customisation is available

for those wanting to work with their own data. Integration in an online environment provides

for collaborative work via shareable web-links, and access to vast repositories of publically

available biodiversity data and phylogenetic trees. Phylolink can map spatial distributions for

individual species or clades, and visualise these by character state or species. Environmental

layers can be intersected with species distributions to map attributes onto phylogenies, and

phylogenetic diversity metrics can be generated for selected trees and areas. Characters can

be mapped onto a tree and ancestral character states for nodes reconstructed. Connecting

biodiversity and phylogenetic knowledge through online open source platforms provides

wider accessibility to evolutionary perspectives on biodiversity data to support research and

conservation decision making.

Page 30: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Amanita is a large, cosmopolitan genus of mushrooms that is well represented in Australia. They

are ecologically important because most species are mycorrhizal with woody plants, and

economically important because some species are edible, whilst others are deadly poisonous.

Species identification is difficult, depending on macroscopic, microscopic and more recently,

molecular characters.

Amanita spp. are included in ALA, but to date, the information there appears to be unreliable. The

names of Australian species are accepted, however the location of some types, such as A.

albifimbriata, A. gracilenta and A. hiltonii are not shown on the maps. Have the type localities not

been picked up by ALA?

There also is a problem with the reliability of some names. From ALA records, A. ananiceps (A.

ananaeceps) occurs along the east coast and in the south west of WA. ALA also gives the accepted

name for A. ananiceps as A. farinacea (east coast distribution), even though these names are not

synonymised in Index Fungorum or Mycobank. In my opinion the images of both A. ananiceps and

A. farinacea on ALA represent more than one species.

Is this a common problem with other poorly known groups of uncharismatic species?

Page 31: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4
Page 32: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4
Page 33: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

The Atlas of Living Australia is the Australian node within the Global Biodiversity Information

Facility (GBIF, http://www.gbif.org/), an international, intergovernmental initiative to

mobilise and organise open data on the recorded occurrence of species in time and space,

including data from natural history collections, field research, environmental genomics,

citizen science and literature. Since its establishment in 2001, GBIF has provided leadership

in delivering tools, standards and best practices for mobilising biodiversity data for free and

open use by the research community and to support policy applications. As of April 2016, this

resource brings together around 650 million data records from data-holding institutions and

organisations around the world. Developments in the GBIF infrastructure and services since

2014 have included use of Digital Object Identifiers to enable all data to be cited clearly, and

adoption of Creative Commons licences to ensure clarity around supported use. These

changes have consolidated GBIF’s relevance and function as the global reference resource for

primary evidence of species distribution.

GBIF has recently expanded its data publishing software and data indexing systems to

incorporate additional data elements from projects which follow consistent standardised

methodologies to sample or survey species within a taxonomic group. Examples of such

projects include vegetation plot surveys, bird atlases, butterfly or reef transects, malaise

sampling, microbial ecogenomics, etc. Further work will be required to catalogue

methodologies referenced in these data and to model relevant level of effort, species

detectability, etc., but this small enhancement to GBIF's existing processes allows users to

discover and access those datasets which offer the greatest opportunities for statistical

comparison.

GBIF’s priorities in the next period are to target the most significant gaps and to address

quality issues which limit the usefulness of some datasets. Two major applications are of

particular importance. The first is to organize all data to enable the best possible assessment

of species distributions and change over time. The second is to ensure that GBIF, in

collaboration with other biodiversity informatics initiatives, offers an effective platform to

assist taxonomists and collection managers to accelerate description of global

biodiversity. Both of these applications depend on improved integration of a broad range of

biodiversity and environmental information.

Through the ALA, Australia has been a significant contributor to GBIF’s work and to the

development of other national nodes. A number of countries are benefiting from adoption

of ALA software and tools. The ALA has an ongoing opportunity to offer global leadership and

innovation in building a global-scale knowledgebase for biodiversity.

Page 34: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Two broad analytical approaches have dominated efforts to assess potential impacts of climate

change on the spatial distribution of biodiversity, and to thereby inform policy formulation,

planning and management aimed at addressing these impacts. The first, and most widely applied,

approach focuses on modelling shifts in the distribution of particular biological entities – mostly

individual species, but also higher-level aggregations such as species assemblages or functional

groups. The second approach focuses instead on analysing spatiotemporal patterns in climate

alone – e.g. projections of climatic stability, velocity of climate change, and novel and disappearing

climates, along with consideration of such patterns in adaptation strategies aimed at “conserving

nature’s stage”. An arguable strength of this approach is its utility for addressing regions and/or

components of biodiversity where the data and understanding required to explicitly model

biological responses are lacking. However, analyses of climate alone do not recognise that the

level of biological change expected to be associated with a given amount of change in a climatic

attribute can vary markedly between biological groups, environments, and biogeographic regions.

We here describe how these sources of variation can be accommodated by combining best-

available location records for large numbers of species (e.g. from ALA or GBIF), with statistical

modelling of spatial turnover in species composition. This modelling is used to scale (transform)

multidimensional climate space, such that distances within this transformed space correlate as

closely as possible with observed levels of biological turnover. We then use recent analyses

underpinned by this approach to demonstrate how it can serve as a third major option for

assessing and addressing climate-change impacts on biodiversity, effectively occupying the middle

ground between explicit modelling of shifts in biological distributions, and analyses based on

spatiotemporal patterns in climate alone.

1 CSIRO Land and Water, PO Box 1600, ACT 2601, Australia

2 NSW Office of Environment and Heritage, University of New England 2351, Australia

Page 35: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

The Brigalow Belt in Queensland is a crucial bioregion in Australia: it is highly modified for

coal, coal seam gas, agriculture and grazing; and at the same time, it’s recognised as a National

Biodiversity Hotspot. We determined the most cost-effective management actions to protect

the biodiversity of the Brigalow Belt bioregion over the next 50 years following a priority

threat management assessment. We first identified the threatened species in the bioregion

using the Atlas of Living Australia. Then stakeholders and experts proposed 12 feasible

strategies to improve the persistence of those threatened species. Finally, we prioritised

those strategies according to their ecological cost-effectiveness. The optimal strategies’

combination under limited budgets was also assessed. If no management strategies are

implemented, 21 species out of 179 are at risk of becoming functionally lost from the

bioregion. Implementing all the 12 strategies effectively (average annualised cost of

$57m/year) could avert the loss of 12 of these species. The Atlas of Living Australia was

essential for our project as it allowed us to easily collate a database of the species in the

bioregion and their threat status. This database was the basis of our study as it helped us to

determine the number and type of experts involved in our project.

Page 36: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Eucalypt species show a variety of strategies for population persistence through fire and

other disturbances. These range from death of individuals with population replacement

through post-fire seedling recruitment, to species in which individuals survive fire via

resprouting from a variety of organs. We used all records of Eucalyptus from selected

bioregions across southern Australia held in the Atlas of Living Australia database to

examine spatial patterns of richness, endemism and composition in two distinct post-fire

response types: mallee (resprout from a lignotuber) and non-resprouting (fire-killed). The

distribution and evolution of eucalypt diversity in mallee and non-resprouting post-fire

response types is best understood in terms of a centre of species richness and endemism on

the south coast of Western Australia with richness and endemism then declining to the

north and east. Spatial analysis of mallee species composition showed four continental-scale

groupings; two unique to south-western Australia, a Great Victoria Desert-centred group

and a south-east Australian group with a clear biogeographical connection across the

coastal Nullarbor gap.

Page 37: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Ecological restoration is recognized as a strategy for climate change adaptation. Yet, ongoing

and projected environmental changes are seldom considered in seed provenance planning,

which is likely to undermine the long-term success of restoration efforts. In this study, we

used species distribution models (SDM) to, first, understand the potential impacts of climate

change on plant distributions and, second, facilitate the decision-making process for selection

of seed provenance strategies to be used in ecological restoration, as applied to five south-

western Australian riparian species as a case study. We advocate that SDM can be used in a

structured, spatially explicit fashion to provide a foundation where different lines of evidence

relevant to seed provenance can be transparently analyzed, and more intuitively understood

by land managers and practitioners. The spatial insights gained on species current and

projected distribution ranges, climate change rates and directions, can be supplemented with

other key information, such as the species adaptive genetic variation, and field-collected or

remotely sensed data of climate-driven plant health decline, to help choose the provenancing

strategies most adequate for each species and restoration project in a climate change context.

Page 38: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Abstract

Aim: The range of environmental conditions that species are known to occupy - their realised

environmental niches - are important indicators of ecological specialisation and biogeographic

history. We test three hypotheses regarding the distribution of species niches across environmental

space: 1) species niche widths are independent of their niche positions along moisture, temperature

and soil nutrient gradients; 2) species niche widths and positions along each gradient are

independent of their functional trait values, and; 3). niche volumes are independent of niche

positions and traits.

Location: Wet Tropics biogeographic region, Australia (WT).

Methods: We summarised geographic records for all ~ 4300 Wet Tropics vascular plant species using

the Atlas of Living Australia. For all records for each species, we calculated the niche width (95th -5th

percentile) and niche position (median of environmental values). Summaries were made in three

important environmental dimensions for plant physiology, using interpolated climate and soil

surfaces: annual rainfall (mm), maximum temperature of the warmest period (°C) and total soil

nitrogen (%). Public-access databases were used to quantify maximum plant height (m), and leaf

width and length measurements were used to estimate leaf area (cm2).

We tested hypotheses 1) and 2) using spatially constrained randomisations of linear and polynomial

regressions for all species (n = 2,285) and trees (n = 745), running separate models for each

environmental dimension. Hypothesis 3) was tested using structural equation models of combined

niche volumes for tree species as the primary response variable, and niche positions and traits as

the predictors, running separate models for each trait.

Results: For both all species and trees, temperature niche widths were independent of niche

positions. However, species niches were narrower in drier and less fertile environments. Similarly,

species whose niches were centred in wetter, cooler and more fertile parts of environmental space

were more likely to be taller and have larger leaves. Only a small amount of variation in niche volume

was explained by niche positions and traits.

Potential implications: Our results demonstrate that while the diverse flora of the Wet Tropics are

not strongly specialised across temperature space, they display greater specialization towards drier

and less fertile conditions. Future studies could test how the biogeographic origins of different taxa

comprising the flora influence the degree of environmental specialistion between species.

a School of BEES The University of New South Wales,

UNSW Sydney, NSW 2052 Australia b CSIRO Land and Water Flagship

Canberra ACT 2601 Australia

Page 39: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Databases such as the Atlas of Living Australia (ALA) give users access to massive amounts of

species location data. The aggregation, and public access, of such data provide the

opportunity to investigate spatial distributions of species, families or ecological communities

at previously impossible scales. Such databases are particularly useful when investigating

patterns amongst ecological communities, where large volumes of species data are required.

However, much of the data in these databases consist of species location records and do not

contain any direct information about where a species has not been found. Ideally, information

on species absences should be included when making inferences about the spatial distribution

of species or communities. Robust filtering of presence-only data can help to address this

problem, but is often time consuming, requiring many hours of user input to complete, and

may be difficult for areas/communities that are extensive or outside of the user’s knowledge

base. Bypassing the need for robust filtering of this type of data would greatly improve

useability for large-scale community level analyses.

Here we present a method for modelling spatial turnover in species composition by

transforming predictions made from binary classifications of pairs of species observations.

Using the mechanics of Generalised Dissimilarity Modelling (GDM; a method for modelling

site-pair differences in species composition), we take pairs of species observations, rather

than site level observations, and model the probability that a pair of species, randomly

selected from two sites, will be the same species or different species. We are then able to

back-transform this probability into an estimate of dissimilarity in species composition

between any two locations, thus bypassing the need to work with complete, robustly filtered,

community data. Recently we used this method to model the compositional dissimilarity of

three biological groups (vertebrates, plants and invertebrates) at 1km2 resolution globally,

using the entire GBIF database. Comparisons with traditional GDMs fitted against ALA

datasets for Australia show good agreement between the predictions from each method,

suggesting that this new method is a good solution to modelling community-level information

using presence-only data such as that accessible through the ALA.

Page 40: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Bush Blitz (www.bushblitz.org.au) is Australia’s largest nature discovery project – a multi-year,

multimillion dollar partnership to document the plants and animals in hundreds of properties

across Australia’s diverse landscapes. Since the program began in 2010 Bush Blitz has discovered

about 600 new and undescribed species and has added thousands of species to what is already

known – providing baseline scientific data informing the protection and management of

biodiversity. CSIRO is supporting the program through data-driven analyses of biological survey

gaps to enhance local targeting and national coverage of field surveys. Four biological groups are

used as indicators of survey completeness – vascular plants, reptiles, amphibians and land snails –

informing the selection of new areas where predominantly vascular plants and invertebrate

surveys are conducted. The specialised analytical framework, which uses the principle of

complementarity, combines the biological survey data with spatial environmental data at 250m

resolution to capture heterogeneity across a range of scales. Resulting layers of information

support subsequent area identification for further investigation of survey potential taking into

account field logistics. This ‘big data’ application has only recently become feasible through data

aggregations such as the Atlas of Living Australia (www.ala.org.au) and the Australian Ecological

Knowledge and Observation System (www.aekos.org.au). While data for plants and vertebrates

are well represented, there is a need to focus more effort on mobilising invertebrate data. We

discuss our experience in accessing and using such aggregated biological data and outline where

further integration of ecological data would enhance their effectiveness for such meta-

applications.

1. Biodiversity, Ecosystem Knowledge and Services (CSIRO Land and Water Flagship), PO Box 1600, ACT, Australia2. Australian Biological Resources Study (Department of the Environment), National Botanical Gardens, Canberra, ACT,Australia 3. Scientific Services Division (Office of Environment and Heritage), University of New England, Armidale, NSW,Australia 4. The Australian Museum, College St, Sydney, NSW, Australia5. Landscape Intensification (CSIRO Land and Water Flagship), Townsville, QLD, Australia

Kristen leads a multidisciplinary group of scientists within a program of research focussed on a sustainable Australia where biodiversity prospers and ecosystems meet the needs of all people. She has a background in biodiversity modelling, conservation assessment and systematic conservation planning incorporating process knowledge of ecosystems and whole landscape perspectives.

Page 41: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Abstract

The Biodiversity and Climate Change Virtual Laboratory (BCCVL) is a ‘one-stop modelling shop’

funded by National eResearch Collaboration and Resources Project (NeCTAR) that simplifies the

process of modelling biodiversity and climate change. The BCCVL achieves this by connecting the

research community to Australia’s national computation infrastructure by integrating a suite of

tools in a coherent online environment. Users can access biodiversity and environmental data

from the Australian Living Atlas, global online datasets or upload their own datasets, perform data

analysis with a suite of 17 different algorithms, and easily visualise, interpret and evaluate the

results of the models.

ALA’s model of providing access to data through standardised and robust machine to machine

(m2m) interfaces or Application Programming Interfaces (APIs) has enabled the BCCVL to easily

integrate, expand functionality and to innovate using species data. Well described and published

data with API access removes some of the challenges associated with integrating and displaying

data in individual applications. Commonly, data access needs to be negotiated with individual

providers; metadata does not allow for easy visualisation or access by machine learning

algorithms; machine to machine data transfer is difficult or not fast enough for modelling

applications and; there is limited ability to manage provenance on frequently updated datasets.

Easy access to other non-species related data (e.g. terrestrial, aquatic, marine, climate,

environment) through m2m interfaces is necessary for continued innovation and development of

modelling applications.

This presentation will showcase how the BCCVL utilises ALA data and its software infrastructure to

enable researchers to investigate, explore and accelerate biodiversity and climate change

research. It will also explore the potential for expanding data available through m2m interfaces

and highlight some like initiatives and applications.

[email protected]

Page 42: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Poster Session

Page 43: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Banksia woodland plant communities are very important habitats within the Perth Metropolitan

Region and include a high diversity of plants that are challenging to identify. A basic photographic

catalogue for banksia woodland plants was also developed which functions as a basic tool to

identify plants without the need for botanical knowledge (flower colour, flowering time and

growth form). While identifying plant that occur in banksia woodland is challenging enough, land

managers and community groups require ecological and biological information about plants for

restoration projects. It is easy to produce lists of local native species for restoration projects with

ALA’s search tools, but such lists will often include a mixture of upland and wetland species, as

well as species that cannot be propagated. The inclusion of functional attributes from existing

databases should help to alleviate these problems. The Banksia Woodland Restoration Project has

gathered key information relevant to restoration projects that includes:

1. The relative importance of plants in natural habitats (abundance, cover and frequency).

2. Survival data for seeding or planting in restoration sites.

3. Seed availability, germination data, seedling morphology and propagation results.

4. Fire impacts, fire recovery strategies and germination from soil seed banks.

5. Pollinators and seed production.

Ecological data can also be categorised for taxa above plant species. For example, a global

database has assigned the mycorrhizal status and other nutrition strategies for plants using

phylogeny. This allows “diversity maps” for plant nutrition strategies to be produced using ALA

tools. In summary, the Banksia woodland Restoration Project has gathered important information

about plant species, such as the restoration potential, response to fire and seed biology, that is

required by land managers so should be accessible via species databases.

Page 44: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Maritza Roberts is a young Nunggubuyu lady working with the Aboriginal Yugul Mangi Rangers in

the proposed SE Arnhem Land Indigenous Protected Area. Basil Murrungun is a young Nunggubuyu

man working the Ngukurr Yangbala (Young people’s) project associated with the Ranger program.

We have been working with the ALA and Emilie Ens (Macquarie University) to contribute more

Aboriginal knowledge to the ALA website to show that biodiversity knowledge is not only about

scientific knowledge. Aboriginal people have deep and intimate knowledge of plants and animals

and Country. Although some knowledge transmission has been disrupted due to white settlement,

we are working hard to re-learn language names for plants and animals and associated cultural

knowledge. We go out bush and do plant and animal surveys and record stories with old people.

We also work with the Ngukurr Language Centre to uncover old language names from the language

dictionaries, like those for Marra, Ngandi and Ritharrngu. We are compiling this knowledge in a SE

Arnhem Land plant and animal book which we will transfer into the new ALA Profiles Pages. As

young people, we like using new technology to bring traditional language and knowledge alive.

Bringing more Aboriginal knolwedge into the Atlas of Living Australia:

Page 45: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

The ALA is a valuable resource for scientists and citizen science practitioners that enables the

collection and sharing of information for biodiversity assessments. An area of increasing

interest to the ALA unit is to explore the role of information management platforms in

bridging boundaries between knowledge systems. This ALA pilot is one of two that explores

the potential opportunities of two-way exchange between western science and Indigenous

knowledge. In particular we focus on indigenous perspectives of risks and benefits of

knowledge exchange and consider some of the enabling conditions for a two-way exchange.

Our pilot study conducted with Olkola people on their country highlights the importance of

supporting on-going efforts of economic sustainability that include intellectual property

considerations, engaging customary and other governance structures, to ensure proper

consultation occurs and consideration of the cultural importance of plants, animals and places

in data collection. There is great potential to expand the use of the ALA with Indigenous

communities in ways that are mutually beneficial however this effort also needs to allow for

time to consult within groups and resources to support Traditional Owners to make informed

decisions about two-way exchange.

1. CSIRO Land and Water

2. Olkola Traditional Owner and elder

3. Tropical Indigenous Ethnobotany Centre

Page 46: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Desert Aboriginal people have accumulated rich observations and knowledge of species and their

complex ecologies. But many forces threaten Aboriginal knowledge and desert ecosystems

important to Aboriginal people.

A collaborative ecological knowledge research project on Arandic lands over eight years focuses

on species of importance to Central Australians. Many species are useful for food and medicine.

Others have profound totemic values. For example, Arandic people believe specific caterpillars

formed the mountains and geographic sites around Alice Springs. What are these species? What is

their ecology? Why would caterpillars be so important to Arandic people? So far, the ALA has

helped address the first of these questions. The ALA could provide an important opportunity to

support knowledge sharing. But there are challenges.

Aboriginal knowledge was once carefully managed. How to navigate tensions between the urgent

need to retain Aboriginal ecological knowledge and the risks when their knowledge is opened to

the public domain? Can the ALA portray sophisticated cultural knowledge of multiple species that

are inter-related to each other? Steps to address some of these challenges are identified. Real,

accurate and comprehensive examples that show human-ecological inter-relationships are vital.

Steps to ensure collaboration, informed decision-making and benefits to Aboriginal people are

outlined.

Ayepe-arenye or White-lined hawkmoth in animal form and geological form (left photo and compilation © Fiona

Walsh)

Page 47: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Banksias are iconic and ecologically key members of the flora of south-west WA. Modelling has

also suggested that they face severe future threats as their climatic envelopes move polewards in

response to anthropogenic climate change, potentially leading to catastrophic range contractions

and extinction of many species. The southwest has already experienced substantial climate

change, including a 15% reduction in winter rainfall in many areas since the 1970s. Hence, it may

be expected that range contraction may already have commenced for some Banksia species.

Banksia also has an unusually rich distributional data set, as a result of a highly successful citizen

science project – the Banksia Atlas – in the mid-1980s. This project used more citizen scientists to

revisit key locations for 6 target Banksia species 30 years after the Banksia Atlas, to attempt to

detect early stages of climate-change-induced range erosion. Findings suggest that range erosion

cannot yet be detected. The greatest risk in the period 1985-2015 to persistence of Banksia

species is ecological dysfunction, as measured by weed invasion. This is consistent with current

theory suggesting that maintaining ecological resilience is important in adapting to the undoubted

threat of climate change for Banksias in the near future.

Page 48: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

The DigiVol crowdsourcing transcription based data capture platform established and managed by the Atlas of Living Australia and the Australian Museum has now been running for 5 years. Starting out as a prototype to see if it would actually be sustainable it has exceeded expectations and become a significant contributor to the liberation of the data held in the form of specimen labels, notebooks and images from collections held in institutions around the world.

The strength of DigiVol lies not just in its ability to attract and retain citizen scientists as contributors but also in its open and versatile template based model which enables anyone from anywhere in the world with a collection of images to build their own online transcription project, known as a virtual expedition in DigiVol. This results in the ability for DigiVol to provide capacity building in two ways, in terms of the capacity of volunteers to become citizen scientists whose skills grow as they spend more time on DigiVol and the capacity of institutions around the world to build and maintain their own digitisation programs with DigiVol. I will talk about the power of the DigiVol infrastructure for institutions and organisations big or small to build and manage their own transcription and tagging projects through DigiVol.

Page 49: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

The Shire of Kalamunda, located in the eastern metropolitan region of Perth, Western Australia,

manages local biodiversity and recreation values on over 400 parks and environmental reserves

across the extent of the local government authority (some 324 square kilometres).

To compliment this work, community and friends group members have been trained in and continue

to use the Atlas of Living Australia (OzAtlas) to record species occurrences in many local parks and

bushland reserves within the Shire of Kalamunda. This data is subsequently used by the online

community to get a real sense of the biodiversity values within the shire, distribution of weeds and

what species are located nearby using the AL and OzAtlas mobile app.

But is there more information available to local governments that is not yet on the Atlas? You bet

there is!

In 2016, volunteers working with the Shire of Kalamunda began capturing data that had been

historically stored in local reserve assessments, management plans and other electronic files and

organising this data into the standard ALA templates to be uploaded to the OzAtlas.

Using local volunteers to harvest this historical data has already tripled the available data at one

site. As this project continues, we anticipate more data on other reserves will become available via

the OzAtlas and provide a clearer picture of the local and regional biodiversity values within our

Shire to residents, researchers and other users of the OzAtlas platform.

Without doubt there is similar historical data within other local government authorities across

Australia and this small pilot project aims to demonstrate that local authorities across Australia can,

with very little additional investment. Supporting volunteers to provide our communities with local

biodiversity information via the OzAtlas will have a positive impact on range of stakeholders across

all of Australia.

Volunteers, working directly with local governments, for the benefit of our nation’s biodiversity –

truly inspirational stuff!

Page 50: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

The Atlas of Living Australia provides access to data and tools that can be used to address

the big questions in ecology and evolution, not just those pertaining to understanding

Australian flora and fauna. This is evidenced by publications in international, high impact

factor journals that use the Atlas and its tools. We have been harnessing the data and tools

available through ALA to implement active learning projects for third-year biology students

at The University of Queensland. Students test general ideas, such as the universality of the

latitudinal gradient of species diversity, and design ways that their hypotheses about species

distributions can be tested. Using data and tools in ALA, students also propose research

questions that have not been previously addressed and then conduct analyses to try to

answer those questions. Examples include whether the Great Dividing Range is a major

generator of species diversity, whether climate is more important in species disjunctions

than dispersal limitation, and whether traits are more divergent in sympatric sister species

pairs than those in allopatry. ALA is an exceptional resource for research at both the

professional and acquiring expertise levels.

Page 51: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

For almost two decades it has been recognised that tertiary students require a range of new

literacies that fall outside the traditional cannon. Commonly collected together under the banner

of '21st century literacies', these include: proficiency, flexibility and fluency in the use and

application of technological tools; design and sharing of information with global communities for a

variety of purposes; managing, analysing and synthesizing of multiple streams of simultaneous

information; creation, critiquing and evaluation of multimedia texts; and attention to the ethical

dimensions of these tasks.

However, contemporary learning and assessment tasks in science generally have yet to tackle

these skills head on. In this presentation, I will describe how I have designed and implemented

assessments that use the ALA and the EU Scratchpads for Biodiversity programs to address 21C

literacies, and discuss the philosophy that underpins my approach. I will also consider

impediments to the wider implementation of this approach to student learning, and how

overcoming them can enrich not only students' learning but also the tools and their user and

developer communities.

Page 52: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

.

The long standing partnership between the Australian Biological Resources Study (ABRS) and the

Atlas of Living Australia (ALA) has culminated in several important projects that provide online

access to a reliable list of names and taxonomy for the plants and animals of Australia. The ABRS

facilitates taxonomic research, and produces and disseminates authoritative biodiversity

information on behalf of the Australian science community. This includes providing authoritative

and current information on nomenclature and taxonomy for organisms occurring in Australia,

which is used by ALA to provide the names you see in the applications on their website. This

presentation will provide an introduction to the ABRS and its work, and discuss three key projects

undertaken in partnership with the ALA:

1. The Australian Faunal Directory is the taxonomic database that provides detailed and

authoritative information on the nomenclature and currently accepted taxonomy for

protozoan and metazoan animals in Australia. Names are used by ALA as the basis for

connecting and displaying various types of data from other sources (e.g. museum collection

data/occurrence records etc.).

2. The Australasian eFlora platform is being progressed in partnership with the Council of Heads

of Australasian Herbaria, ABRS and the ALA. This exciting new project aims to build

infrastructure that will support the collaborative creation of eFlora/s, to increase content

sharing capabilities, allow for distributed editing, reduce duplication of effort and shorten the

time to publication for taxonomic treatments

3. The National Species List (NSL) provides infrastructure to deliver aggregated nomenclatural

and taxonomic information. Currently, the NSL delivers the Australian Plant Names Index, the

Australian Plant Census, and AusMoss. It is has the potential to become the central repository

for all names and taxonomic checklists/classifications of organisms occurring in Australia. The

NSL also provides data sharing web services in line with international standards, which

increases the accessibility and usability of the data.

Page 53: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Access to biological literature is essential to taxonomic research and our understanding of

biodiversity. It is the primary source of species descriptions, biological data, ecosystem

profiles, distribution maps, and geological and climatic records. Much of the world’s biological

literature is now available digitally online, providing researchers with far more convenient

access than they have ever had in the past to the publications that underpin their work.

The Atlas of Living Australia (ALA) is committed to providing access to digital literature,

including the digitisation of Australia’s biodiversity heritage literature and to making this

literature freely available online. To this end, the ALA has, since 2010, funded an Australian

collaboration to contribute to the Biodiversity Heritage Library (BHL). Led by Museum

Victoria, this collaboration has now digitised and contributed to BHL over 150,000 pages from

the library collections of Australia’s museums and herbaria. This year, the ALA has further

strengthened its relationship with the BHL by taking up a role in governance by becoming a

BHL Member.

However, despite the wealth of taxonomic literature now available online and the ALA’s

commitment to adding to it, the ALA does not link to the full text digitised publications from

its own website. Literature citations for accepted names, synonyms and taxon concepts are

drawn into the ALA website from the National Species Lists – the Australian Faunal Directory

(AFD) and the Australian Plant Names Index (APNI)/Australian Plant Census (APC), but these

citations are simple plain text.

If these citations could be made active and ‘clickable’ by the addition of a URL to the

underlying data, this would allow users to click through to the published text online – in the

BHL or in any open access publication. In this paper we will discuss how such links could be

made, how the data could be gathered and, most importantly, why creating these links would

be of value to the taxonomic community, and to ALA users more generally.

Page 54: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

The North West Atlas was created in response to the need for more comprehensive and

accessible information on environmental and socio-economic data on the greater north-west

marine region. It provides the infrastructure and tools to promote the free and open

exchange of information to support science, policy making and public understanding. As

such, the North West Atlas is a web portal developed to not only access and share

information, but to celebrate and promote the biodiversity, heritage, value, and way of life

of the greater Northwest region.

To achieve these goals, the North West Atlas provides:

• A web portal to share information, data and maps online;

• A regional information repository;

• Access to research conducted within this area;

• Access to information for informed decision making; and

• A user friendly site to engage people to explore and learn about the region.

The North West Atlas project builds on the e-Atlas project for the Great Barrier Reef and the

Ningaloo Atlas covering Ningaloo World Heritage Area. It is a partnership between

government organisations, non-government organisations, researchers, industry, and

community groups to improve our understanding and raise awareness of the greater north-west

marine region. The continued cataloguing and description of data via the North West Atlas

has the potential to facilitate important future research outputs based on gap analysis and

meta-analysis and collaborations with larger research programs such as the National

Environmental Science Program and Western Australian Marine Science Institution.

Funding for the North West Atlas has been provided by PTTEP Australasia (a wholly-owned

subsidiary of PTTEP, the Thai national petroleum exploration and production company), the

Australian Institute of Marine Science (AIMS) and the National Environmental Science

Program.

Page 55: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

A workshop in Sao Paulo March 8-11 brought together the leaders of the TDWG/GBIF Interest

Group on Data Quality and of the associated Task Groups. The results of this work will be

presented to TDWG in Costa Rica in December.

Data Quality Interest Group and Task Group 1 (Arthur Chapman) focussed largely on using a

Framework for Data Quality to prepare Data Quality Profiles based on Use Cases presented

by the GBIF Task Groups on Fitness for Use for Agrobiodiversity and for Species Distribution

Modelling. As part of this process, some time was also spent on preparing a Controlled

Vocabulary that will be compatible with the Data Quality Profile currently being prepared by

the W3C.

Task Group 2 (Lee Belbin) focused on the tests and associated assertions that are used to scan

data submitted to the ALA, GBIF and other Data Publishers. 152 tests were collected from the

ALA, GBIF, BISON, iDigBio and other Data Publishers. An example of such as test “coordinate

uncertainty was not supplied with the record”. The workshop rationalized the attributes of

the tests/assertions and agreed to develop a standard suite of tests/assertions that should be

used by all Data Publishers. This would assist users to determine Fitness for Use of any subset

of data.

Task Group 3 (Miles Nicholls) developed a method to capture data quality use cases in an

accessible manner consistent with the frame work developed in Task Group 1. Through

several iterations a simple form was developed that allows a detailed description of the data

quality constraints in a particular use case to be captured. Once collected the data quality

components across a series of use cases can be analysed to identify key quality metrics and

validate the utility of data quality assertions.

Page 56: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

The Spatial (Research) Portal (SP) of the Atlas of Living Australia continues to develop; filling

gaps, addressing bugs, increasing consistency and adding new features.

New layers produced as a result of analyses can now be re-used in other SP tools. For example,

a layer of the probability of occurrence of a species from a Spatial Prediction Model using

MaxEnt can be used in scatterplots or GDM layers in an area classification. The Area Reports

have been updated and extended to cover lists (http://lists.ala.org.au) that include invasives

and threatened species. The PDF Area Report provides an extensive summary of the biological

and environmental conditions of any area. Area of Occupancy (AOO) and Extent of

Occurrence (EOO) as used in the IUICN Red List criteria have been added. AOO and EOO can

be used to help determine changes in species distributions and current status of taxa. A new

tool enables a comprehensive environmental comparison between any set of points. The

values of all (~500) layers are sampled at all points and the result is displayed in the legend

area and can be exported as a CSV file for further analysis.

There are also some very neat functions that many don’t seem to know about. For example,

cross tabulations of contextual layers and weekly updates of Australia wide layers on

occurrence density, species richness and endemicity.

Page 57: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4
Page 58: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4
Page 59: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4
Page 60: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Title First Name Last Name Organisation Title Phone Email

Dr Kym Abrams Western Australian Museum [email protected]

Mrs Amanda Barker Private Individuals [email protected]

Ms Sarah Barrett DPaW [email protected]

Mr Ben Bayliss DPaW [email protected]

Mr Lee Belbin Private Individuals Director 03 6265 9990 [email protected]

Dr Rachel Binks DPaW [email protected]

Mrs Hanouska Bishop Private Individuals [email protected]

Ms Roxane Blackley

Queensland Murray-Darling Basin

Committee Spatial Analyst [email protected]

Mr Peter Brenton Atlas of Living Australia Team Leader 02 6246 5813 [email protected]

Dr Mark Brundrett DPaW [email protected]

Mr Hugh Burley CSIRO OCE PhD Student 02 6246 5902 [email protected]

Ms Ryonen Butcher DPaW [email protected]

Dr Margaret Byrne DPaW Science and Conservation Director [email protected]

Mr Ainsley Calladine Private Individuals [email protected]

Mr Alex Chapman Gaia Resources Consulting Scientist 08 9227 7309 [email protected]

Mr Arthur Chapman

Australian Biodiversity Information

Services [email protected]

Mr Simon Checksfield CSIRO Team Leader 02 6246 4314 [email protected]

Ms Karen Clarke DPaW [email protected]

Dr Anne Cochrane DPaW [email protected]

Mr Geoff Cockerton Western Botanical Managing Director 08 9274 0303 [email protected]

Dr Margaret Collins DPaW [email protected]

Dr Lyn Cook University of Queensland School of Biological Sciences 07 3365 2070 [email protected]

Mr Colin Crane DPaW [email protected]

Mr Ian Cresswell CSIRO Research Director 03 6232 5213 [email protected]

Ms Eleanor Crichton

Department of Environment, water and

Natural Resources (SA) Science Resource Coordinator 08 8222 9480 [email protected]

Mr Russell Cumming Private Individuals [email protected]

Dr Emma Dalziell Botanic Gardens & Parks Authority [email protected]

Miss Karmelina Daniels Private Individuals [email protected]

Mr Robert Davis DPaW [email protected]

ATTENDEES

Page 61: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Title First Name Last Name Organisation Title Phone Email

Mr Mick Davis Shire of Kalamunda [email protected]

Dr Elaine Davison Curtin University [email protected]

Dr Peter Davison Private Individuals [email protected]

Dr Gaynor Dolman Western Australian Museum Manager & Research Scientist 08 9212 3878 [email protected]

Dr Nick dos Remedios Atlas of Living Australia Team Leader 02 6246 4434 [email protected]

Dr Janet Farr DPaW [email protected]

Dr Simon Ferrier CSIRO Team Leader 02 6246 4191 [email protected]

Mrs Nicole Fisher CSIRO Research Technician 02 6246 4261 [email protected]

Mr Paul Flemons Australian Museum [email protected]

Ms Sue Fyfe ABRS [email protected]

Dr Neil Gibson DPaW [email protected]

Dr Lesley Gibson DPaW [email protected]

Mr Paul Gioia DPaW

Principal Research Scientist,

Information 08 9219 9067 [email protected]

Dr Carl Gosper CSIRO JV Employee 08 9333 6442 [email protected]

Dr Greg Guerin University of Adelaide Postdoctoral Fellow [email protected]

Dr Mark Harvey Western Australian Museum

Senior Curator & Head, Dept of

Terrestrial Zoology 08 9212 3737 [email protected]

Ms Judith Harvey DPaW [email protected]

Mr Shane Herbert Private Individuals [email protected]

Mr Donald Hobern Global Biodiversity Information Facility Executive Secretary +45 35321472 [email protected]

Mr Hamish Holewa Griffith University

Mr Michael Hope Atlas of Living Australia Team Leader 02 6246 4117 [email protected]

Miss Tara Hopley DPaW [email protected]

Dr Andrew Hoskins CSIRO Postdoctoral Fellow 02 6246 5902 [email protected]

Dr John Huisman Western Australian Herbarium Acting Curator 08 9219 9137 [email protected]

Dr Joel Huey Western Australian Museum Research Scientist 08 9212 3738 [email protected]

Ms Diana Jones Western Australian Museum Executive Director 08 9212 3715 [email protected]

Mr Tony Jupp The Nature Conservancy Aridlands Project Manager 08 9287 8307 [email protected]

Mrs Nicole Kearney Museum Victoria [email protected]

Ms Janine Kinloch DPaW [email protected]

Dr Lisa Kirkendale Western Australian Museum Curator (Mollusca) 08 9212 3747 [email protected]

Dr John La Salle Atlas of Living Australia Group Leader 02 6246 4262 [email protected]

Ms Tania Laity Department of the Environment 02 6274 1490 [email protected]

Mrs Naomi Lawrence

Department of Primary Industries,

Parks, Water & Environment (TAS) Senior Scientist-Natural Values Atlas 03 6165 4328 [email protected]

Dr Kristina Lemson Edith Cowan University Undergraduate Courses Coordinator 08 6304 5369 [email protected]

Dr Esther Levy DPaW [email protected]

Page 62: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Title First Name Last Name Organisation Title Phone Email

Mr Wolfgang Lewandrowski Private Individuals [email protected]

Dr Cheryl Lohr DPaW [email protected]

Ms Vanda Longman DPaW [email protected]

Ms Pethie Lyons CSIRO Research Scientist 07 4059 5017 [email protected]

Dr Terry Macfarlane DPaW [email protected]

Dr Adrienne Markey DPaW [email protected]

Ms Sharon McArthur Private Individuals 0498 981 525 [email protected]

Ms Kelli McCreery Private Individuals [email protected]

Mr Richard McLellan

Northern Agricultural Catchments

Council Chief Executive Officer 08 9938 0102 [email protected]

Miss Margarita Medina University of Canberra PhD student 02 6201 2267 [email protected]

Dr Melissa Millar DPaW [email protected]

Dr Ben Miller Private Individuals [email protected]

Ms Toni Moate CSIRO Strategist 03 6232 5209 [email protected]

Dr Cordelia Moore Australian Institute of Marine Science [email protected]

Mr Basil Murrungun Ngukurr Yangbala Project

Mr Miles Nicholls Atlas of Living Australia Company Contractor 02 6218 3431 [email protected]

Mr Gregory O'Donnell Private Individuals [email protected]

Dr Kym Ottewell DPaW [email protected]

Ms Cheryl Parker DPaW [email protected]

Miss Julia Percy-Bower DPaW [email protected]

Miss Juliana Pille Arnold Private Individuals [email protected]

Mr Adrian Pinder DPaW [email protected]

Dr Rebecca Pirzl Atlas of Living Australia Team Leader 02 6246 4108 [email protected]

Dr Rocio Ponce-Reyes CSIRO Postdoctoral Fellow 07 3833 5709 [email protected]

Miss Tanya Porter Western Australian Museum [email protected]

Mr Gavin Price BHP Billiton

Dr Cristina Ramalho University of Western Australia Postdoctoral Fellow 08 6488 4565 [email protected]

Mr Damien Rathbone University of Western Australia [email protected]

Dr Holly Raudino DPaW [email protected]

Mr Ben Richardson WA Herbarium

Ms Maritza Roberts Yugul Mangi Rangers

Dr Dan Rosauer Australian National University Postdoctoral Fellow 02 6125 1028 [email protected]

Mr John Ross Private Individuals [email protected]

Ms Lore Schlichting Private Individuals [email protected]

Mr Daniel Schoknecht Western Australian Museum [email protected]

Ms Tina Schroeder University of Adelaide [email protected]

Dr Kelly Shepherd DPaW [email protected]

Page 63: Australia -   · PDF fileSchool of Animal Biology, The University of Western Australia, 35 Stirling . Highway, Crawley, WA 6009, Australia 4

Title First Name Last Name Organisation Title Phone Email

Mr Saurabh Shrivastava

Australian Genome Research Facility

Ltd Account Manager [email protected]

Mr John Silver Rangelands NRM Operations Manager 08 9192 5771 [email protected]

Dr Ursula Smith Museum Victoria [email protected]

Mrs Felicity Smith Private Individuals [email protected]

Dr Ashley Sparrow CSIRO Principal Research Scientist 08 9333 6451 [email protected]

Mr Ralph Talbot-Smith Private Individuals [email protected]

Ms Cate Tauss Private Individuals [email protected]

Dr Kevin Thiele DPaW Curator 08 9219 9128 [email protected]

Miss Keisha Thompson Private Individuals [email protected]

Miss Faye Thompson Private Individuals [email protected]

Dr Stephen van Leeuwen DPaW Assistant Director, Science 08 9219 9042 [email protected]

Dr Genefor Walker-Smith Museum Victoria [email protected]

Ms Elycia Wallis Museum Victoria [email protected]

Ms Fiona Walsh CSIRO Research Officer 08 8950 7145 [email protected]

Ms Heather Walsh Atlas of Living Australia Administration Support Officer 02 6246 4364 [email protected]

Dr Haylee Weaver Department of the Environment Scientific Officer, Fauna 02 6250 9434 [email protected]

Dr Bruce Webber CSIRO Team Leader 08 9333 6802 [email protected]

Dr Juliet Wege DPaW [email protected]

Dr Kristen Williams CSIRO Group Leader 02 6246 4213 [email protected]

Mr Allan Wills DPaW [email protected]

Ms Elisa Wood-Ward DPaW [email protected]

Prof Andrew Young CSIRO Facilities Director 02 6246 5318 [email protected]

Mr Peter Zurzolo

Western Australian Biodiversity Science

Institute Chief Executive Officer