Saturday, September 2, 2017

Having fun with biodiversity databases

If you have ever professionally used a biodiversity database you will soon have noticed that we still have a long way to go before they are as reliable as we would like them to be.

Today I looked into the Atlas of Living Australia records for Senecio australis (Asteraceae). Except for a rather odd specimen from South Africa the distribution records look like this:

What do we have here? First, the four Australian mainland records all appear to be misapplications of the name. The Flora of New South Wales, for example, does not even mention the species, so I think we can safely assume it does not occur in Australia at all.

Second, the record in the middle of the top of the map is right in the ocean, no matter how closely we zoom in. If we look into its details, we see that it was collected on Norfolk Island, which is the cluster of red dots to its right, so somebody must have got the coordinates rather wrong.

Third, there is a cluster around Auckland, on New Zealand's North Island. I am not sure if Norfolk Island and North Island is a plausible area of distribution for this species, but it may well be. Zooming in closer to Norfolk Island, however, ...

... it looks as if somebody had played darts after having had a few too many beers. ALA informs us dryly under the section data quality tests, "habitat incorrect for species". No kidding. Or as my wife joked, unwilling to believe that the coordinates would be so badly off for such a large percentage of the specimens, "is there a fish that is also called Senecio australis?"

These are the problems that we are dealing with, more generally.
  • Whenever we do a study using data from biodiversity databases, as we increasingly do, we have to be very careful about cleaning the data. The main issues are outdated taxonomy, misidentifications, spatial data entry errors (which are particularly easy to recognise if an outlier record is exactly ten degrees away from a known occurrence), and imprecise spatial data. Just think of what it would do to species distribution modeling if we uncritically accepted all the records for Senecio australis.
  • While we can identify obvious mistakes while using a database, the data are "ground-truthed" in the actual specimens in some herbarium or museum, and the policy is usually (and quite sensibly) that the database won't update until a correction is made to that specimen in its home institution and then filters through from there. But many institutions do not have the resources to update data just because somebody sent them an eMail pointing out that their specimen is misidentified or that they made a data entry error; many herbaria on the planet are so understaffed that even the word understaffed is a euphemism. What is more, even if a database allows a registered user to annotate a record with corrections, the information may not necessarily flow back to the institution holding it, depending on whether somebody thought to set up such procedures or not.
  • Overall, Australia actually has excellent data quality, the Atlas of Living Australia actually allows annotations to be made, and several important Australian herbaria actually have the staffing to update their data. What I am saying is that this is as good as you can have it at the moment. It is much more difficult in many other parts of the world, and of course it would be good if we could have the same or better data quality for those areas.
Also, perhaps it is best not think too much about records that are not specimen-based but "human observations" or photos submitted by random people. There are, obviously, non-taxonomists whose knowledge of the flora is extensive, and citizen science can be awesome, but I have also seen several cases one the lines of "aaargh ... this is so misidentified it is not even the right tribe of the family, and now the database is using it as the profile picture of this nationally significant weed species!"

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