Towards a continent-wide ecological site condition database using calibrated expert evaluations.

A cost-effective way of undertaking comprehensive, continental-scale, assessments of ecological condition is needed to support large-scale conservation planning, monitoring, reporting, and decision-making. Currently, cross-jurisdictional inconsistency in assessment methods limits the capacity to scale-up monitoring. Here we present a novel way to build a coherent continent-wide site-level ecological condition dataset, using cross-calibration methods to integrate assessments from many observers. We focus on the use of condition assessments from individual expert observers, a currently untapped resource. Our approach has two components: (1) a simple online tool that captures expert assessments at specific locations; (2) a process of calibrating and rescaling disparate expert evaluations that can be applied to the data to provide a consistent dataset for use in conservation assessments. We describe a pilot study, involving 28 experts, who contributed 314 individual site condition assessments across a wide range of ecosystems and regions throughout continental Australia. A correction factor for each expert was used to rescale the contributed site condition assessment scores, based on a set of 77 photographic images, each scored for their condition by multiple experts, using a linear mixed model. Our approach shows strong promise for delivering the volumes of data required to develop continental-scale reference libraries of site condition assessments. Although developed from expert elicitation, the approach could also be used to harmonize the collation of existing condition datasets. The process we demonstrate can also facilitate online citizen scientists to make site condition assessments that can be cross-calibrated using contributed images.

Phylolink: phylogenetically-based profiling, visualisations and metrics for biodiversity.

SUMMARY: Phylolink is a research collaboration toolkit through which biodiversity can be explored from a phylogenetic perspective. It is an update of PhyloJiVE that has been integrated into the framework of the Atlas of Living Australia, including its spatial portal. Phylolink connects phylogenetic tree nodes with species occurrence records, environmental data, and species trait information. Features new to Phylolink allow users to upload and download spatial datasets, store files and link to the ALA spatial portal, improve graphics and provide the novel ability to analyze environmental attributes of species and clades distributions. Species richness and phylogenetic diversity comparisons can be made among geographic areas. The result is a powerful way of combining data to generate flexible and customizable visualizations, profiles and metrics for biodiversity. AVAILABILITY AND IMPLEMENTATION: Phylolink is available at the Atlas of Living Australia, http://phylolink.ala.org.au/. It works on any browser and users can select from a range of stored phylogenetic trees and spatial datasets, or upload their own.

Towards global data products of Essential Biodiversity Variables on species traits.

Essential Biodiversity Variables (EBVs) allow observation and reporting of global biodiversity change, but a detailed framework for the empirical derivation of specific EBVs has yet to be developed. Here, we re-examine and refine the previous candidate set of species traits EBVs and show how traits related to phenology, morphology, reproduction, physiology and movement can contribute to EBV operationalization. The selected EBVs express intra-specific trait variation and allow monitoring of how organisms respond to global change. We evaluate the societal relevance of species traits EBVs for policy targets and demonstrate how open, interoperable and machine-readable trait data enable the building of EBV data products. We outline collection methods, meta(data) standardization, reproducible workflows, semantic tools and licence requirements for producing species traits EBVs. An operationalization is critical for assessing progress towards biodiversity conservation and sustainable development goals and has wide implications for data-intensive science in ecology, biogeography, conservation and Earth observation.

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database.

BACKGROUND: Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The 'Biomes of Australian Soil Environments' (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function. FINDINGS: BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project's data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the 'Atlas of Living Australia'. CONCLUSIONS: Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.