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The Atlas of Living Australia (ALA) is a biodiversity data repository focused primarily on observations of individual life forms. The basic unit of data at the ALA is an occurrence record. Occurrence records note what species is found where and when and are standardised by ‘Darwin Core’ methodology (see data standards for more information).
Because biodiversity data are collected from many different sources and across time, they may be provided to us in a variety of different formats. Species names and groups are one component of this dynamism – changing over time and place: inconsistent and conflicting due to new researcher discoveries and disagreements. As a result, species names and groups need to be updated in our database and possible occurrence records of the same species (with conflicting and varying names) congregated – otherwise we risk presenting incomplete or scattered data of one species. This article presents the process used by the Atlas of Living Australia in which different courses of names are collected and transformed into a standardised form of taxonomy.
The ALA uses scientific names and taxonomic trees for specific purposes. The ALA matches names to build an index of occurrence records by species: this works by joining like with like, building an index tree, enabling people to find records across higher taxa. If you wanted to find all records of birds, this search translates to “find me all records indexed to class:AVES”. In addition to this there is a search index of names, data sources, localities, etc, helping us find what we are looking for.
Figure 1. Recipe book analogy, it’s all about classifying, thinking of taxonomy as a cookbook to index recipes.
The ALA does not aim to provide the absolute truth in taxonomy – yet something that is consistent within itself for all records to have a place.
For example, some records:
- Come from the 19th century or even earlier and contain names that no longer fit with our current understanding of biology. Here the ALA takes a ‘best fit’ approach, and this can get messy as a record/species could logically fit into two different current taxa, however a record cannot belong to more than one.
- Come from outside of Australia (from expeditions) referring to species that do not occur in Australia. The ALA cannot import a worldwide taxonomic tree and is only interested in Australian species. However, the name is always present, and people can still find these records.
- Contain only vernacular (common) names which can be shared between multiple species.
The ALA does not exclude records and identifications just because they look incorrect. If something looks incorrect to you and you have reasoning for this, you can flag an issue on the occurrence record page. This will inform the data provider and it is under their jurisdiction to make changes. Currently, the ALA is only a data aggregator.Records are instead marked with data quality metrics. Depending on the application of the data, this data may need to undergo further data quality checks.
How it works
To encompass the wide range of data types/quality/shifting taxonomy the ALA:
1. Build a taxonomic tree where each taxon concept has a place in the tree.
What’s a taxon concept?
Firstly what’s a taxon: A taxonomic group of any rank, such as a species, family, or class
A taxon concept: A set of physical, genealogical, phylogenetic or other biological properties or characters of organisms used to define the abstract boundaries of a ‘taxon’ that collectively distinguish it from other taxa.
There are many taxonomic trees, however the ALA takes trees predominately from the Australian Faunal Directory (AFD), Australian Plant Name Index (APNI), Australian Plant Census (APC) and the New Zealand Organisms Register (NZOR).They have some gaps, and in this case, are supplemented with other sources. See Figure 2 for information on the sources and the order of priority.
What's a taxonomic tree?
Known as a phylogenetic tree: a branching diagram that represents evolutionary relationships among organisms (see Figure 4)
Figure 2. Order of priority for building a taxonomic tree at the ALA. This is: 1) AusFungi, 2) AusMoss, 3) AFD, 4) APNI and APC, 5) NZOR, 6) APNI (names only), 7) CAAB 8) CoL, 9) ALA lists.
Naming authority merging
Where sources disagree or double up, a merging step resolves this. If there is disparity in classification between NZOR and AusFungi then the AusFungi classification will take precedence. However, if there is disparity between NZOR and CoL, then NZOR will be used. If, however, the species is only present in CoL, then this classification will be used.
Figure 3 displays an example of a species Malassezia pachydermatis that has two different names under naming authorities: you can see that the AusFungi name takes precedence for the naming of this species. Information about the naming authority used is displayed directly below the species name, and additional information is in the names tab.
Figure 3. Example of a species with conflicting naming from different naming authorities. AusFungi naming takes precedence over NZOR and the ALA uses the AusFungi name of Malassezia pachydermatis instead of Pityrosporum pachydermatis.
2. Build an index of names where each name is then mapped onto a place in the taxonomic tree
This includes synonyms (names for species that now go by a different name) and vernacular names (commonly used for species), see Figure 5. Due to the dynamism of species names this is not a simple process, this index must be able to be updated as species are reclassified or even discovered.
Figure 4. A schematic displaying what a phylogenetic tree looks like and how species might be indexed into the ALA. This phylogenic tree’s information comes from the Australian Faunal Directory for Ornithorhynchus anatinues (Platypus). The top right-hand corner of the schematic displays a recipe analogy for taxonomy.
3. Process incoming occurrence records by trying to match the supplied names against the index.
Records that are submitted with the most current taxonomic name of the species are identified with an “exactMatch” (Figure 5) in the system, and all the fields can be filled in automatically.
Figure 5. Comparison table of an inputted record for Ornithorhynchus anatinus that’s been processed by its scientific name and additional information attributed to the record.
Old names, common or vernacular names are treated as synonyms in the ALA, and the record is re-classified to appear with the current taxonomic name. The initial inputted name of an occurrence record can still be found, this information is located in the taxonomy box. Figure 6 shows the supplied name was “Macropus giganteus giganteus” and was adjusted in the processing phase, with Figure 7 displaying the comparison table shown in Figure 6.
Figure 6. An example of an incorrectly inputted record that was adjusted in the ALA system to align with the current accepted naming for Macropus giganteus (Eastern Grey Kangaroo).
Figure 7. Comparison table for a record that was submitted with an accepted synonym of a name for a species, showing the original value and the processed value.
- Maintaining a large indexable database is difficult, especially when the backbone of the system is ever-changing.
- The dynamic nature of taxonomy means we have to have systems for processing old names, synonyms, etc.
- The ALA uses taxonomic trees from other sources and creates an index, which we then use to catalogue all incoming records.
- The ALA does not own the data that are provided to us, we aggregate them. This means if there is an issue with a record it can be flagged, but it’s up to the data provider to update it.
Why can’t I find a species I know exists?
While the ALA goes to considerable effort to aggregate available information about all Australian species, there are some circumstances in which the ALA may not display information about a species you are interested in. These include:
- The species may have changed
- The species is not listed in any of the courses of the ALA’s species names, e.g. it may be very newly described, or the name is a manuscript or phrase name.
- The spelling used may be different from that officially recognised
- The common name used may not be recognised by the ALA
Why are Dingoes not represented in the Atlas?
The ALA draws its taxonomic information from several sources, for animals this is predominately the Australian Faunal Directory, who currently consider the dingo a synonym of Canis familiaris. The AFD’s page on C. familiaris describe why Dingoes are currently classified with common dogs. The standard definition of a species is a group of living organisms capable of interbreeding to produce viable offspring. By this definition, since Dingoes and ordinary common dogs can breed together, they belong in the same species.
We recognise that one might still want to search for Dingoes and not other common dogs which are all classified as C. familiaris. People who provide records of Dingoes to the ALA can also specifically say that they are Dingoes. This is stored as the supplied common name-
- click here to perform a search for records in the ALA that specifically include "Dingo" as a name.
Want more information?
If you dive deeper and look at the names section of ALA’s Canis familiaris species page you’ll see that in the past Dingoes have been called Canis dingo, Canis familiaris australasiae, Canis australiae, Canis macdonnellensis, Canis dingoides and even Canis lupus dingo.
Here are some recent papers which explore the phylogeny of the Dingo:
Field, M.A., Yadav, S., Dudchenko, O., Esvaran, M., Rosen, B.D., Skvortsova, K., Edwards, R.J., Keilwagen, J., Cochran, B.J., Manandhar, B. and Bustamante, S., 2022. The Australian dingo is an early offshoot of modern breed dogs. Science advances, 8(16), p.eabm5944. https://doi.org/10.1126/sciadv.abm5944
Jackson, S.M., Fleming, P.J., Eldridge, M.D., Archer, M., Ingleby, S., Johnson, R.N. and Helgen, K.M., 2021. Taxonomy of the Dingo: It’s an ancient dog. Australian Zoologist, 41(3), pp.347-357. https://doi.org/10.7882/AZ.2020.049
Why are there duplicate species?
The ALA is bringing together information from many sources and seeks to link together information provided under different scientific names, where these names are considered synonyms of a single species. However, many names which should be treated as synonyms are not covered by our data sources.