Last week was Mark’s birthday, so what better time for a trek update?
How does a specimen collected by our field team become a sequenced and described species? Join us on the journey that one specimen took once it was brought through the doors at Biologic.
Field Collection
Malard et al (2002) Sampling Manual for the Assessment of Regional Groundwater Biodiversity. European Project PASCALIS. 1-74
This specimen began its journey as an anonymous member of a Karaman sample. It was collected alongside the Great Northern Highway by Biologic’s subterranean fauna team members Anton Mittra and Dr Phil Runham in February 2021.
A Karaman sample is collected by taking a water sample from the bank of a creek and filtering the water through a fine net to collect the microscopic animals that live there. This is the hyporheic zone, the interface between surface and groundwater. It is also where many stygofauna are found, species that reside in subterranean aquifers.
Back to Headquarters
This Karaman sample is taken back to Biologic Headquarters in Osborne Park for further investigation. The Biologic office is kitted out with all the specialist laboratory equipment our experts need to study the specimens that are collected by our field teams.
The sample is sorted by our staff, with specimens placed into different taxonomic groups for further work.
The sample is rich with subterranean fauna, harboring crustaceans, worms, diplurans, and pauropods. Once sorted, this particular specimen is placed with other members of the order Bathynellacea, an ancient crustacean group with links across the now fragmented Pangean supercontinent. This order often harbors species that have short geographic ranges, and as such, are of special consideration for environmental impact assessments. This vial of bathynellaceans is flagged for further study.
Taxonomy
Enter taxonomists Dr Juliana Pille–Arnold and Dr Giulia Perina, who morphologically identify the specimens using a microscope.
Using specialist knowledge, they can see that these specimens belong to the parabathynellid genus Atopobathynella. However, many species of this group are not yet described, a process that involves having a name and description published in peer-reviewed literature. Not only this, Atopobathynella are very difficult to distinguish based on morphology alone, largely due to the small size of the specimens. In some instances, it can also be attributed to the specimen being damaged or juvenile, meaning it is lacking the characters typically used to distinguish the species. They flagged the specimen for DNA sequencing with our in-house molecular systematics team.
DNA Sequencing
DNA sequence data can be used to directly compare specimens and confirm if they are the same species and provides additional evidence to support taxonomic identification. This makes DNA sequencing an incredibly powerful tool in the biologist’s toolbox and is routinely used in biodiversity studies across Australia. Biologic has the added advantage of an in-house DNA Barcode Library. As of 2026, we have over 10,000 sequences amassed, giving our team considerable power to assess biodiversity values.
In 2025 alone our molecular team logged:
- 3,694 extractions
- 3,193 barcode sequences
- 740 new Operational Taxonomic Units (OTUs; analogous to species)
- An 86% overall success rate from extraction to sequencing.
Sequencing a fragment of DNA from a subsample taken from the Atopobathynella specimen and comparing it to our library of 10,000 available sequences revealed something puzzling.
We found the specimen was related to previous specimens collected in the area but also specimens collected from disconnected catchments further to the north. It was unclear whether we were looking at a cluster of closely related species, or one widespread species. At that point, the genus Atopobathynella was assumed to be short ranging, with 51 known taxa having ranges less than 25 km, and one with a 42 km range. However, if these specimens represented a single species, it was inhabiting multiple disconnected catchments over 80kms which was unexpected.
Scientists Deliberate
What followed was a series of discussions and emails between geneticists, taxonomists, subterranean fauna ecologists and aquatic ecologists, all of whom were attempting to answer one question: was this one widespread species, or many short ranging species?
Publishing a Name
Dr Perina, who originally identified the specimen, decided to reinvestigate all the specimens that fell into this confusing group (at this point made up of five different OTUs based on sequencing). She assessed them morphologically and undertook more DNA sequencing.
The result was published last year in a paper describing 12 new species of the family Parabathynellidae. The data supported a single widespread species, and it was named Atopobathynella pervulgata. Fittingly, Guilia derived the name from the Latin word “pervulgata” meaning widespread. The specimen now lives in the WA Museum’s type collection, and is the voucher specimen for this species, against which all other specimens of this genus can be compared.
That same publication included names dedicated to members of the Biologic team. For anyone who has had a species dedicated to them (known as a patronym), it is a great honour. For the Biologic staff who joined this specimen along its journey, it is rewarding being involved in the scientific process of discovering and naming the biodiversity of this state.
Perina, G., Camacho, A.I., Morgan, L., Lawrie, A., Floeckner, S. & Guzik, M.T. (2025) New species of Atopobathynella, Kimberleybathynella and Hexabathynella (Parabathynellidae, Bathynellacea) from the arid zones of Western Australia. Zootaxa, 5655 (1), 1–103. https://doi.org/10.11646/zootaxa.5655.1.1
