Task 1

Mini lectures

I watched three presentations given as an introduction to the Taxonomy and Identification module (Bulbert, 2023). Questions were posed and the answers given below are from notes taken during these presentations

What did you learn?

Taxonomy is not the same as identification (see later question on difference between the two).

Taxonomy started with Aristotle and progressed to the Linnaeus hierarchical structure which is still in use today. ‘Tree thinking’ now allows us to study the evolution of biodiversity (use of phylogeny and systematics to look at evolutionary relationships).

Taxonomy is important to a range of subject areas such as biosecurity, human health, trade and the economy, conservation and cultural value (Thiele et al., 2021). Classification can help direct resources for conservation.

The number of professional taxonomists is low relative to the number of species that are still to be described. There is a general lack of funding due to an underappreciation by the public and policy makers as to the value provided by taxonomy services.

There are several steps used in taxonomy and identification:

Collection of specimens

This can be passive or active depending on the aim and taxa involved.

• Passive techniques: pitfall traps, intercept traps, pan traps, sticky traps, simulated habitat traps and spring mechanism traps.

• Active techniques: observations, hand collection, beating, sweep netting, suction, butterfly netting (to catch on the wing as opposed to sweep netting), coring, disturbance and fogging.

• Baited/stimulus techniques: light traps, berleze/tungsten traps, prey, dung baits, general baits, chemical baits and pan traps.

• Surrogate techniques such as: camera traps, radar, sound recordings/monitoring, footprint pits, hair snares, scats, foraging signs and eDNA rather than collecting specimens.

A variety of methods of sampling can be used, such as: point sampling, plot, transects, timed and mark capture/recapture.

Identification

It is a good idea to start at the upper taxa level and work down e.g. Order for invertebrates. This allows you to segregate and reduce the number of taxa you are trying to work with to ID to species level.

The UK is slightly unusual in that some much of the taxa have already been described to species level, so identification skills to this level is required. In other parts of the world this would be impossible.

There are many resources that can be used such as taxonomic keys, reference collections, taxonomic experts in the UK and gene-banks. Note that field guides are not great for identification and are mainly good for species recognition rather than identification – it is hard to use a field guide to justify an identification.

Curation

More traditional locations for curation such as herbariums and museums typically have legacy collections and are typically used for morphological research. There are other collections with purposes around resurrection of extinct species e.g. the Tasmanian tiger, or the maintenance of the samples in the event species go extinct e.g. the seed bank in Svalbard. There are other ambitious bio-banks that store tissue, or even gametes and embryos that could be used for resurrection or increasing diversity. Live specimens may be kept in zoos or gardens.

Database

There needs to be meta data when collecting specimens, otherwise it is useless beyond identification. This should include: where, when, who, how (collection technique) and host information if applicable.

There are initiatives to bring together biodiversity data, including the GBIF (Global Biodiversity Information Facility).

Research

Species name/description is a hypothesis. Names can be reconciled but may also be split (which can cause problems for ecologists).

It is a complex and time-consuming process to delineate a species: gathering a breadth of data from numerous specimens, delineate based on concepts of what is a new biological entity and then provide a description. It is important to understand the relatedness (systematics) of the species. Note that there are different definitions of species. The biological concept is the most quoted but doesn’t apply to non-sex-based systems e.g. prokaryotes.

The naming convention used is to state the Genus then the Species in italics e.g. Lotus corniculatus. Then if used subsequently, the Genus is abbreviated e.g. L. corniculatus.

The Linnaeus hierarchy follows: Domain -> Kingdom -> Phylum -> Class -> Order -> Family -> Genus -> Species.

‘Tree-Thinking’

Phylogeny allows us to build a tree to organise species based on shared derived traits, leading back to common ancestors. The roots represent the ancestor lineage and the tips represent the descendants of the ancestor. Nodes indicate a speciation event. Clades are groups of taxa. Note that phylogeny doesn’t necessarily exactly match Linneaus hierarchy.

It allows us to identify convergent evolution, where similar traits have evolved separately in unrelated species. It can be used in epidemiology and to better understand where organisms are closely related.

What can you personally add to the narrative provided by these presentations?

My take-away from these presentations is that taxonomy is a key building block required for the understanding of the organisms around us, yet due to it being very resource-intensive it is not adequately funded to provide the benefit that it could deliver across many different sectors.

As I embark on my ecological career understanding the taxonomy of a wide range of taxa will be invaluable. The scope of this due to the diversity present is a little intimidating but by understanding common taxa and starting at higher levels I hope to build my knowledge further.

Phylogenetics looks to offer interesting insights that will improve our understanding of the relationships between organisms.

What concerns you about the issues around the state of taxonomy?

A large proportion of retired professional taxonomists not being replaced means that knowledge may be lost. Also, reliance on an aging population and volunteers is not good for the discipline.

Underfunding and understaffing will lead to missed opportunities or threats. As the rate of extinction outstrips the rate of species description, this is a cause for concern as we will miss many species that could provide valuable research opportunities that inform important areas such as healthcare. Also, on a personal/moral viewpoint it is saddening that many species that are present now will become extinct before we are even aware of them.

If taxonomic publications are viewed to have less ‘impact’ than publications that rely on them, then funding for more taxonomic research may be even harder to acquire.

Try to articulate the difference between identification and taxonomy

Taxonomy is the classification and characterisation of organisms based on what is known relative to others i.e. describing and classifying organisms. Identification is the use of characters that describe an organism to determine what taxonomic group it belongs to.

Identification therefore relies on organisms having already been described i.e. identification relies on taxonomy; whilst taxonomy is concerned with describing those organisms.

References

Bulbert, M. (2023) ‘BIOL7001: Taxonomy and Identification Mini-taxonomy III’ [Recorded lecture]. BIOL7001: Taxonomy and Identification. Oxford Brookes University. 09 September. Available at  https://brookes.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=cfa918d9-cdbc-4d48-b913-b083012e4b09 (Accessed 03 October 2023)

Thiele, K. R., Conix, S., Pyle, R. L., Barik, S. K., Christidis, L., Costello, M. J., van Dijk, P. P., Kirk, P., Lien, A., Thomson, S. A., Zachos, F. E., Zhang, Z. Q. and Garnett, S. T. (2021) 'Towards a global list of accepted species I. Why taxonomists sometimes disagree, and why this matters', Organisms Diversity & Evolution, 21(4), pp. 615-622. Available at: https://doi.org/10.1007/s13127-021-00495-y.

Bulbert, M. (2023) ‘BIOL7001: Taxonomy and Identification Mini-taxonomy I’ [Recorded lecture]. BIOL7001: Taxonomy and Identification. Oxford Brookes University. 09 September. Available at https://brookes.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=9495895f-56f0-4730-a2a7-b08301103350 (Accessed 03 October 2023)

Bulbert, M. (2023) ‘BIOL7001: Taxonomy and Identification Mini-taxonomy II’ [Recorded lecture]. BIOL7001: Taxonomy and Identification. Oxford Brookes University. 09 September. Available at https://brookes.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=f0daea9e-4f1d-4022-a767-b083011dcf18 (Accessed 03 October 2023)