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The Atlas of Prehistoric Australia · focused on fossil fishes, mammals and birds, respectively....

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is project is supported by the Australian National Data Service (ANDS). ANDS is supported by the Australian Gov- ernment through the National Collaborative Research Infra- structure Strategy Program. anks to the entire team at the Atlas of Living Australia (CSIRO), without whom this would not have been possible. Further thanks in particular to Doug Palmer and Michael Hope. Reference: Dirk Megirian, Gavin J. Prideaux, Peter F. Murray, and Neil Smit (2010) An Australian land mammal age biochronological scheme. Paleobiology: 36 (4) pp. 658-671. Acknowledgments: Help provided by Flinders University and many of its employees proved invaluable on this project, most especially Amanda Nixon, Liz Hall, Chris Carapetis and Yasmine Shaheem. is endeavour honours James Moore (1990-2014) for his enthusiasm and remarkable atten- tion to detail. (JSLM Pictured next to GJP and GAG respectively.) June 2015 Context Over the past three decades, Flinders Palaeontology has been a leader in improving our understanding of the unique his- tory of Australia’s vertebrates. Researchers have accumulated a wealth of knowledge on the occurrences of species through time and space, along with images of specimens and sites, scanning data and field notes. However, much of the infor- mation has remained within datasets created ad hoc by indi- vidual researchers. With funding from ANDS via the Major Open Data Collections Project program, we synthesised these data to form the foundation of a broadly useful, publi- cally accessible, expandable database. Data Fossils collected from field sites arrive at Flinders requiring stabilisation, identification and registration. Once studied, they are deposited in museum collections. Researchers oſten visit these museums to study other specimens. In the process, they compile large datasets usually tailored to address specific questions. Outcomes are published in peer-reviewed litera- ture or presented in student theses, but oſten in an abstracted form, aſter which researchers move on to other projects. One shortfall is that many of the data accumulated during the life of these projects are not readily available to other researchers, especially those outside of Flinders. Similarly, three of us (JL, GP, TW) have generated exhaustive locality and species data matrices from published literature focused on fossil fishes, mammals and birds, respectively. ese were largely developed for individual use, although much of the Database of Australasian Vertebrate Occur- rences (DAVO) formed the backbone of the Australian land mammal age biochronological scheme (Megirian et al. 2010). ese datasets are stored in spreadsheets, which are unwieldy for searching and presenting data compared to genuine data- base repositories. Flinders researchers also utilise new technologies, such as x-ray computed tomography (µCT), which is very useful for studying fossils difficult to analyse using traditional tech- niques (e.g., fossilised soſt tissue in embedded limestone) or generating quantitative measurements of tissues of differing densities (e.g., tooth enamel and dentine). is research gen- erates terabytes of raw data, which creates challenges for data storage. Approach An extensive search for a potential database management system was carried out with priorities on the following criteria: using commercial applications or open source and their related costs, upload and download capabilities, search capabilities, data link- ing, potential longevity, and accessibility. e stand-out option was partnering with the CSIRO to develop a node of the Atlas of Living Australia (ALA). e project drew inspiration from existing environments designed for sharing palaeontological data, including the Paleobiology Database, but adopted a more multidisciplinary, open-source approach through the use of Darwin Core (DwC) and Global Bio- diversity Information Facility (GBIF) standards. e bulk of the project focused on aggregating data from different sources. Our original occurrence datasets for specimens, species, localities and references were assessed for errors and re-mapped to DwC ter- minology. A series of filters and error checkers were applied that help maintain data integrity, accuracy and conformability to pre- viously mapped data. Significance e APA provides a medium for biologists, palaeontologists and archaeologists to explore the evolution and ecology of the Australian fauna. It adds time depth to the ALA, extends the known geographic ranges of existing species and contributes palaeoenvironmental information to better comprehend the evolution and distribution of extant species. e APA will be of intrinsic interest to researchers focused on how Australian ani- mals respond to climatic changes, providing a palette of infor- mation useful for aiding our mitigation of climatic impacts. e integration of the APA into the ALA ultimately makes our datasets on past biodiversity available to a global community of researchers focused on understanding and preserving cur- rent and future biodiversity. Future Flinders Palaeontology sees the APA as an ongoing entity and plans to add additional data as it becomes available. Col- laborators within Australia have already been contacted and expressed interest in contributing to the APA to enhance and extend the data available. Palaeontology is a highly interna- tional field, with many Flinders researchers working with col- leagues in other countries. is project will provide a platform for further international collaborations. Aim & Objectives e core aim was to create an open-access, online repository for Flinders Palaeontology datasets. To achieve this required the development of metadata content for existing spreadsheets and data upload to Research Data Australia. Key objectives were to make data more readily searchable, to enhance content visually and structurally, to integrate it into an existing database frame- work, and to build in capacity for expansion. Outcomes e key outcome of this project has been the development of the Atlas of Prehistoric Australia (APA; apa.ala.org.au), a node of the ALA, which is in turn a node of GBIF, a global initiative encouraging free and open access to biodiversity data. e data is now accessible and subjectable to complex interrogation. It is also now easily downloadable in formats that are inter- operable and compliant with accepted discipline standards, such as DwC. apa.ala.org.au Check it out. Figure 1. Collecting raw data. Excavation of Pleistocene vertebrates, including megafauna, Tight Entrance Cave, Western Australia. Figure 2. µCT scan of a Devonian placoderm fish (Bothriolepis) skull embed- ded in limestone, showing early evolution of lateral line. Figure 3. One of our datasets, DAVO. Our problem was how to go from this, to something easily accessible and useable (see Figure 4). Figure 4. APA Home page and Search result page showing all the fossil localities. Each locality marked may represent multiple species occurrences. Contact: grant.gully@flinders.edu.au gavin.prideaux@flinders.edu.au john.long@flinders.edu.au trevor.worthy@flinders.edu.au Grant A. Gully, Gavin J. Prideaux, John A. Long, Trevor H. Worthy & James S.L. Moore e Atlas of Prehistoric Australia is a storehouse of information on the occurrences of organisms through time and space. It is the deep-time add-on to the Atlas of Living Australia, and emphasises the continuum between past and present, and the valuable role that historical data on taxonomy, ecology and environment can play in improving our understanding of Australia’s unique biota. The Atlas of Prehistoric Australia GAG PALAEONTOLOGY
Transcript
Page 1: The Atlas of Prehistoric Australia · focused on fossil fishes, mammals and birds, respectively. These were largely developed for individual use, although much of the Database of

This project is supported by the Australian National Data Service (ANDS). ANDS is supported by the Australian Gov-ernment through the National Collaborative Research Infra-structure Strategy Program.

Thanks to the entire team at the Atlas of Living Australia (CSIRO), without whom this would not have been possible. Further thanks in particular to Doug Palmer and Michael Hope.Reference: Dirk Megirian, Gavin J. Prideaux, Peter F. Murray, and Neil Smit (2010) An Australian land mammal age biochronological scheme. Paleobiology: 36 (4) pp. 658-671.

Acknowledgments: Help provided by Flinders University and many of its employees proved invaluable on this project, most especially Amanda Nixon, Liz Hall, Chris Carapetis and Yasmine Shaheem. This endeavour honours James Moore (1990-2014) for his enthusiasm and remarkable atten-tion to detail. (JSLM Pictured next to GJP and GAG respectively.) June 2015

ContextOver the past three decades, Flinders Palaeontology has been a leader in improving our understanding of the unique his-tory of Australia’s vertebrates. Researchers have accumulated a wealth of knowledge on the occurrences of species through time and space, along with images of specimens and sites, scanning data and field notes. However, much of the infor-mation has remained within datasets created ad hoc by indi-vidual researchers. With funding from ANDS via the Major Open Data Collections Project program, we synthesised these data to form the foundation of a broadly useful, publi-cally accessible, expandable database.

Data

Fossils collected from field sites arrive at Flinders requiring stabilisation, identification and registration. Once studied, they are deposited in museum collections. Researchers often visit these museums to study other specimens. In the process, they compile large datasets usually tailored to address specific questions. Outcomes are published in peer-reviewed litera-ture or presented in student theses, but often in an abstracted form, after which researchers move on to other projects. One shortfall is that many of the data accumulated during the life of these projects are not readily available to other researchers, especially those outside of Flinders.

Similarly, three of us (JL, GP, TW) have generated exhaustive locality and species data matrices from published literature focused on fossil fishes, mammals and birds, respectively. These were largely developed for individual use, although much of the Database of Australasian Vertebrate Occur-rences (DAVO) formed the backbone of the Australian land mammal age biochronological scheme (Megirian et al. 2010). These datasets are stored in spreadsheets, which are unwieldy for searching and presenting data compared to genuine data-base repositories.

Flinders researchers also utilise new technologies, such as x-ray computed tomography (µCT), which is very useful for studying fossils difficult to analyse using traditional tech-niques (e.g., fossilised soft tissue in embedded limestone) or generating quantitative measurements of tissues of differing densities (e.g., tooth enamel and dentine). This research gen-erates terabytes of raw data, which creates challenges for data storage.

ApproachAn extensive search for a potential database management system was carried out with priorities on the following criteria: using commercial applications or open source and their related costs, upload and download capabilities, search capabilities, data link-ing, potential longevity, and accessibility. The stand-out option was partnering with the CSIRO to develop a node of the Atlas of Living Australia (ALA).

The project drew inspiration from existing environments designed for sharing palaeontological data, including the Paleobiology Database, but adopted a more multidisciplinary, open-source approach through the use of Darwin Core (DwC) and Global Bio-diversity Information Facility (GBIF) standards. The bulk of the project focused on aggregating data from different sources. Our original occurrence datasets for specimens, species, localities and references were assessed for errors and re-mapped to DwC ter-minology. A series of filters and error checkers were applied that help maintain data integrity, accuracy and conformability to pre-viously mapped data.

SignificanceThe APA provides a medium for biologists, palaeontologists and archaeologists to explore the evolution and ecology of the Australian fauna. It adds time depth to the ALA, extends the known geographic ranges of existing species and contributes palaeoenvironmental information to better comprehend the evolution and distribution of extant species. The APA will be of intrinsic interest to researchers focused on how Australian ani-mals respond to climatic changes, providing a palette of infor-mation useful for aiding our mitigation of climatic impacts. The integration of the APA into the ALA ultimately makes our datasets on past biodiversity available to a global community of researchers focused on understanding and preserving cur-rent and future biodiversity.

FutureFlinders Palaeontology sees the APA as an ongoing entity and plans to add additional data as it becomes available. Col-laborators within Australia have already been contacted and expressed interest in contributing to the APA to enhance and extend the data available. Palaeontology is a highly interna-tional field, with many Flinders researchers working with col-leagues in other countries. This project will provide a platform for further international collaborations.

Aim & ObjectivesThe core aim was to create an open-access, online repository for Flinders Palaeontology datasets. To achieve this required the development of metadata content for existing spreadsheets and data upload to Research Data Australia. Key objectives were to make data more readily searchable, to enhance content visually and structurally, to integrate it into an existing database frame-work, and to build in capacity for expansion.

OutcomesThe key outcome of this project has been the development of the Atlas of Prehistoric Australia (APA; apa.ala.org.au), a node of the ALA, which is in turn a node of GBIF, a global initiative encouraging free and open access to biodiversity data.The data is now accessible and subjectable to complex interrogation. It is also now easily downloadable in formats that are inter-operable and compliant with accepted discipline standards, such as DwC.

apa.ala.org.au

Check it out.

Figure 1. Collecting raw data. Excavation of Pleistocene vertebrates, including megafauna, Tight Entrance Cave, Western Australia.

Figure 2. µCT scan of a Devonian placoderm fish (Bothriolepis) skull embed-ded in limestone, showing early evolution of lateral line.

Figure 3. One of our datasets, DAVO. Our problem was how to go from this, to something easily accessible and useable (see Figure 4).

Figure 4. APA Home page and Search result page showing all the fossil localities. Each locality marked may represent multiple species occurrences.

Contact: [email protected] [email protected] [email protected] [email protected]

Grant A. Gully, Gavin J. Prideaux, John A. Long, Trevor H. Worthy & James S.L. Moore

The Atlas of Prehistoric Australia is a storehouse of information on the occurrences of organisms through time and space. It is the deep-time add-on to the Atlas of Living Australia, and emphasises the continuum between past and present, and the valuable role that historical data on taxonomy, ecology and environment can play in improving our understanding of Australia’s unique biota.

The Atlas of Prehistoric AustraliaG A G

P A L A E O N T O L O G Y

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