Atlas Of Living Australia Research Articles

VicFlora: a dynamic, service-based Flora

VicFlora (https://vicflora.rbg.vic.gov.au), launched in September 2016, combines the Flora of Victoria and the Census of Vascular Plants of Victoria. VicFlora is used by government agencies, conservation agencies and consultancies: analytics indicate that on weekdays VicFlora is used by between 200 and 250 people. Content of VicFlora can be updated inside the system, so changes will be live as soon as they are made, the keys coming from KeyBase and the maps using data from the Australasian Virtual Herbarium (AVH) and the Victorian Biodiversity Atlas (VBA), both obtained through Atlas of Living Australia (ALA) web services. Corrections and value-adding to the maps are done through annotations. There have been requests from government and consultancies for the ability to use content from VicFlora in their own applications. Therefore, web services have been created that give access to all content. New versions of VicFlora will use these same services. It is the intention that names and taxon concepts for VicFlora will be managed in the National Species Lists (NSL) and accessed through NSL web services.

Introduction of the Living Atlases workshop

Since 2010 the Atlas of Living Australia (ALA) gives information on all the known species in Australia and contributes to the Global Biodiversity Information Facility (GBIF). To provide a suitable framework for national needs, ALA and GBIF worked together and created a technical community around the platform developed by ALA. This one is called Living Atlases. Through this community, members can be helped during the installation and configuration of modules based on this architecture by the ALA technical team or other participants. Since 2013, several beginner and advanced workshops have been made focusing on various ALA tools. Because the level of the community members has increased, some former trainees have become new trainers. Added to these technical workshops, we have been able to present and demonstrate our work during international conferences with always the main goal to show how re-using an existing software can be motivating and stimulating as well as be part of a living community. Indeed, ten institutions members to Living Atlases launched their national data portal. In the future, we expect more GBIF nodes to put their software in production (Andorra, Germany, Benin, Luxembourg, etc.). During this introduction, we will present the community by showing past events as well as presentations done during previous conferences. Then, we will describe the human aspect of the project by presenting the international community and listing some key points of the software such as internationalization or customization. We will finish it by explaining the future of the Living Atlases community and how you can contribute and be part of it.

Living Atlases: tips and advices

Atlas of Living Australia (ALA), Australian node of the Global Biodiversity Information Facility (GBIF), provides information on all the known species in Australia. Since 2010, ALA has developed an open source framework providing different tools to help users from various sectors. The ALA technical team, with the help of GBIF, has reorganized the architecture of ALA tools into several modules to help other institutions to re-use the code. The three first sessions of this workshop focuses on data indexation, occurrence search engine and metadata registry. The last session delves into more technical subjects with hands-on demonstration of installing an instance of the portal (also known as ALA-demo*1) using Ansible scripts. In addition to this, sharing of experience regarding the customization of data portals and building a name indexer using national checklists will be covered. Finally, we will present others modules such as ALA4R*2, project allowing R users to access data and resources hosted by a platform based on ALA, or Image service*3, tiling and image repository tool.

Documentation about Atlas of Living Australia tools: how to find information

ince 2013, a community has been created around Atlas of Living Australia (ALA) tools *1, an open source platform developed by the Australian node of the Global Biodiversity Infrastructure Facility (GBIF) (also named ALA). Its primary goal is to provide information on Australian biodiversity. Its modular architecture has been designed to help institutions worldwide reusing it for their data portals. Eight ALA-like platforms are currently in production around the world with different levels of implementation. Until date, five international workshops have been organized focusing on numerous subjects ranging from first step to install the data portal to configuring the advanced spatial portal. This has helped the community to grow significantly. GBIF France, the French node of the GBIF established in 2006, has been part of the Living Atlases community since 2014. GBIF France is an active members of ALA community and is one of the eight institutions with ALA based data portal in production. The main object of this presentation is to describe the documentation part writing by the ALA team with the help of the community, and located on the ALA GitHub account *2. Thanks to this tool, anybody can read the different sections of the documentation. It is organized by themes and highlight important subjects for new or advanced users such as architecture, how to install your own demonstration ALA data portal, internationalization, customization, etc. A huge part of this manual is feedbacks from advanced developers to help newcomers by presenting their own architectures, customization and tips. In this presentation, we will demonstrate how the documentation is a key point to help the community to be durable and efficient. We will also present its central thread and how we manage all elements around it. Finally, we will discuss about the wiki by defining good practices to request more information about a specific theme or add tips from your own experience.

Impacts of climate change on eucalypt distributions in Australia: an examination of a recent study

ABSTRACTA recent study examined the possible impacts of climate change on 657 Australian eucalypt species in the period to 2085 using species distribution modelling (SDM). The study predicted that ‘within the next 60 years the vast majority of species distributions (91%) across Australia will shrink in size (on average by 51%)’. The purpose of the present paper is to demonstrate some of the strengths and weaknesses of this previous study. Its main strength is that it identifies relatively hot and dry areas of species distributions that may be vulnerable under climate change. Its main weakness is that the individual analyses tend to overestimate the areas of species natural distributions. Consequently, the predicted percentage losses of species distribution areas are unreliable. To illustrate the problem the freely available Atlas of Living Australia (ALA) is used examine two contrasting species (Eucalyptus diversicolor and E. nitens) in detail, so readers will be able to apply similar methods to any eucalypt species of interest. For well-known species a more reliable assessment of likely losses of distributional area under climate change may be obtained by applying the results of the SDM analysis, but assuming that ALA occurrences within 25 km x 25 km areas are an accurate representation of present natural distributions. Using this approach the estimated loss of area of natural distribution by 2085 for both E. diversicolor and E. nitens are less than half the estimates provided by the original paper. For lesser-known species, it is concluded that an additional SDM analysis is required to provide a closer representation of species natural distributions, to which the original SDM climate change results, which attempt to capture some of the species adaptability/plasticity, could be applied.

Identifying particular areas for potential seed collections for restoration plantings under climate change

SummaryA method to assist identifying potential sites for seed collections for restoration plantings is demonstrated using the Atlas of Living Australia (ALA) and an example site near Albury (New South Wales). The mean annual temperature (MAT) and mean annual precipitation (MAP) of the example site are determined using the ALA. Data on likely changes in MAT and MAP are accessed from the ‘Climate Change in Australia’ website. The ALA's ‘define environmental envelope’ function is then used to identify areas currently experiencing conditions similar to the future climatic conditions projected for the site. Species distribution data in the ALA indicate locations where suitable provenances of the chosen species are likely to be present. In the case of trees, satellite images in the ALA can indicate whether isolated trees or extensive stands, that may be genetically diverse, exist at locations of interest. Shrublands, grasslands or wetlands may also be identified from the satellite images. The Monitoring, Evaluation, Reporting and Improvement Tool (MERIT) within the ALA can be used to identify existing trials that may already be using suitable provenances for the restoration site. Some considerations for provenance selection under climate change are outlined, as well as the advantages and limitations of using the ALA for this purpose.

Posting Traditional Ecological Knowledge on Open Access Biodiversity Platforms: Implications for Learning Design

BowerBird is an open platform biodiversity website (http://www.BowerBird.org.au) and a nationally funded project under management of the Atlas of Living Australia (ALA) and Museum Victoria. Members post sightings and information about local species of plants and animals, and record other features of ecosystems. Charles Darwin University's Northern Institute Elder on Country researcher, Kathy Guthadjaka, has shared pictures and information about the biodiversity of her homelands in the Yolŋu community of Gäwa, on Elcho Island in north east Arnhem Land, Northern Territory. The extent to which this knowledge can be exposed in the same way as other open resources, can pose dilemmas about the level of ‘openness’ that is appropriate. Open sharing of educational materials can be promoted as a basic human right. This paper will explore the extent to which traditional knowledge can be made openly available. What are the implications for sharing this knowledge in a westernised context that compartmentalises it, and how can a western academic perspective learn from this knowledge and engage functionally with it for the purposes of learning? The existence of this project on the interface between traditional knowledge and western technocratic information management also has implications for how information is presented and valued.

Using biodiversity databases to verify and improve descriptions of tree species climatic requirements

Understanding tree species climatic adaptability, as well as climatic conditions within their natural distributions, is crucial for managing forests for both commercial and conservation objectives under climate change. Multi-million dollar investments in biodiversity databases are providing forestry professionals with freely accessible tools to carry out these kinds of analyses for many tree species. The climatic requirements of hundreds of tree species have been described in the commercially available Forestry Compendium developed by CAB International, but these descriptions have often relied on expert opinion where information is lacking. It is desirable that descriptions of tree species climatic requirements should, as far as possible, be explicit, quantitative and based on specific observations. This paper describes how the Atlas of Living Australia (ALA) and the Global Biodiversity Information Facility (GBIF) can provide specific observations to assist verifying and, where necessary, improving descriptions of tree species climatic requirements. It focuses mainly on Australian species as the ALA is one of the most sophisticated biodiversity databases currently available for a single country. However, the ALA also has international relevance as Australian eucalypts and acacias are important plantation species in many countries. Data in the GBIF complement the ALA data by providing very useful information on where Australian tree species are growing outside Australia. Analyses of a commercially important species (Eucalyptus nitens) and a lesser-known species (E. botryoides) demonstrate how descriptions of climatic requirements can be verified and, if necessary, improved. However, the general methods described have the potential to be applied to many tree species. Some of the advantages and disadvantages of these systems are discussed and possible improvements are suggested.

A specialist’s audit of aggregated occurrence records: An ‘aggregator’s’ perspective

A recent ZooKeys’ paper (Mesibov, 2013: http://www.pensoft.net/journal_home_page.php?journal_id=1&page=article&SESID=df7bcb35b02603283dcb83ee0e0af0c9&type=show&article_id=5111) has highlighted data quality issues in aggregated data sets, but did not provide a realistic way to address these issues. This paper provides an aggregator’s perspective including ways that the whole community can help to address data quality issues. The establishment of GBIF and national nodes (national aggregators) such as the Atlas of Living Australia (ALA) have integrated and exposed a huge diversity of biological observations along with many associated issues. Much of the admirable work by Mesibov (2013) was enabled by having the data exposed.Data quality, one of the highest priorities for GBIF, the national nodes and other aggregators, depends on both automatic methods and community experts to detect and correct data issues. Not all issues can however be automatically detected or corrected, so community assistance is needed to help improve the quality of exposed biological data. We do need to improve the infrastructure and associated processes to more easily identify data issues and document all changes to ensure a full record is permanently and publicly available.

A specialist’s audit of aggregated occurrence records

Occurrence records for named, native Australian millipedes from the Global Biodiversity Information Facility (GBIF) and the Atlas of Living Australia (ALA) were compared with the same records from the Millipedes of Australia (MoA) website, compiled independently by the author. The comparison revealed some previously unnoticed errors in MoA, and a much larger number of errors and other problems in the aggregated datasets. Errors have been corrected in MoA and in some data providers’ databases, but will remain in GBIF and ALA until data providers have supplied updates to these aggregators. An audit by a specialist volunteer, as reported here, is not a common occurrence. It is suggested that aggregators should do more, or more effective, data checking and should query data providers when possible errors are detected, rather than simply disclaim responsibility for aggregated content.