Standardised taxonomic data for radiocarbon samples

By Joe Roe, 2023-12-21 14:23:23 UTC

Radiocarbon dating can be applied to any type of organic materials. But where possible, archaeologists try to collect an identifiable piece of preserved animal or plant tissue, because knowing what species it came from is often necessary to obtain a reliable date. For example, species with diets high in marine food produce apparent ages older than their true age due to the marine reservoir effect, and this needs to be corrected for. When radiocarbon dates are responsibly published, this taxonomic information will be reported alongside the age determination and other important information about the sample. Most of our source databases recorded this in turn, but practices for doing so varied widely. One author might record a sample of human bone as “Homo sapiens”, where another calls it “human femur” or another “Menschenknochen”. So anyone searching for dates on a particular taxon will find it difficult to predict all the ways it might show up in XRONOS.

To begin to make this data more predictable and usable, earlier this year we began transforming all the taxonomic descriptions in XRONOS to use a standardised scientific nomenclature. We match scientific names to the GBIF Backbone Taxonomy, a standard for all branches of life maintained by the Global Biodiversity Information Facility, ensuring that they fit a single, consistent nomenclature that can be linked to other sources of biodiversity data. We used the GBIF Species API to automatically match as many taxonomic descriptions as possible to begin with, then began the long process of manually reviewing the c. 11,806 taxons that could not be unambiguously related to the backbone taxonomy. Chiara Huwiler, an archaeology and biology student here at Bern, was a huge help here – as of today, we’ve worked through over 2500 unknown taxons.

In standardising the taxonomic data in XRONOS, we assign a single, scientifically accepted taxons at the species level or above to each sample. Many of our source databases recorded common names, paraphyletic groups, and multiple species, or included extra information alongside the taxon. We transformed these to the lowest valid taxonomic rank that unambiguously encompasses the source data, without any additional markers such as “sp.” or “spp.”, and without any subspecies or varieties. We also replaced any names that GBIF considers synonyms (i.e. not part of the currently accepted taxonomy) with the accepted nomenclature, ensuring that all recognised taxons have only a single name in XRONOS.

Sometimes this does mean we lose information. Only a subset of the family Poaceae (grasses) are would be described as samples “cereals”, for example, but this is the lowest valid taxon that includes them all. We think this is a trade-off making to keep the taxonomic data in XRONOS internally consistent and relatable to other sources of scientific data. We also retain the original information in the version history of the record, meaning that it can always be recovered and inspected later.

Taxons that have been matched to the GBIF Backbone Taxonomy are now displayed as full scientific names with a link to the relevant page in GBIF. For example RTD-7313 was derived from a sample of tuber belonging to the genus Bolboschoenus (Asch.) Palla, a.k.a. GBIF name #2718273. Where taxon has not (yet) been matched, the original data from the source is shown, with a flag warning that this taxon is not standardised. This also means that searching for samples from particularly taxons is much easier: here is all 1288 recorded samples of Corylus avellana (hazel/hazelnut), for example.