Introduction

Taxonomy is the science of classifying, naming, and describing organisms based on shared characteristics. The classification of living things, has its origins in ancient Greece and in its modern form dates back nearly 250 years, to Carl Von Linné’s Systema Naturae (1735) where Linnaeus introduced the binomial classification still in use today (Godfray, 2002). The Linnaean taxonomy is a ranked system for categorizing organisms, and the principal ranks in modern use are domain, kingdom, phylum (division is sometimes used in botany in place of phylum), class, order, family, genus, and species. The main objective of this ranked system is to systematize the known diversity of organisms. However, with recent advances in theory, data and analytical technology, modern taxonomy also seeks to reflect the evolutionary relationships among organisms.

Traditional morphology-based taxonomy

Originally, shared morphological characteristics has been the foundation for the organisation of organisms in the Linnaean taxonomy. This includes comparing observable traits—body shape, size, colour patterns and structural features (teeth, bones, flowers, leaves)—alongside comparative anatomy, embryology and analyses of developmental patterns and structural homologies. Many of these morphological traits are easily observable, making this approach both very feasible and available, especially in the field and in the laboratory, but also with specimens in museums collections. Therefore, they remain essential for describing species, diagnosing taxa and identifying fossils.

Limitations of morphological taxonomy

Although morphology-based taxonomy has persisted for centuries, it faces several problems. Linnaeus dramatically underestimated the number of species, and as later naturalists described ever more plants and animals—often unaware of one another’s work—the result was confusion that nearly derailed the whole field in its early days. Today we might call that the first bioinformatics crisis. Nineteenth-century taxonomists, working with the limited tools available, met the challenge with a remarkably effective solution: they created a detailed set of rules governing how species are named and linked to type specimens, how genera and higher ranks are treated, and how disputes over names are settled. Those rules, centered on publications in books and journals, evolved into the modern codes of zoological and biological nomenclature (Godfray, 2002).

In modern times, the expert taxonomist who navigated themselves out of the first bioinformatic crisis, are not present anymore and we are currently in a solid lack of taxonomists housing specialist knowledge about certain taxonomic groups. The term “taxonomic impediment” has been debated for decades now, and the term represents both the insufficiency and inadequacy of the resources put to the service of taxonomy (the taxonomic impediment sensu stricto) and its main consequence, the wide discrepancy between the reality of specific biodiversity and our knowledge of it (the taxonomic gap) (Engel et al., 2021).

Another major limitation with traditional morphology-based taxonomy, is the occurrence of very similar morphologies and cryptic species. Cryptic species are defined as distinct evolutionary lineages that are morphologically very similar (or indistinguishable) but are reproductively or genetically distinct (Struck et al., 2018). As such, reliance on morphology alone can underestimate species diversity. Additional variation in morphologies caused by e.g. environmental plasticity, ontogenetic changes and sexual dimorphisms can cause issues when relying solely on morphological traits for classification. Another issue due to misclassification can also occur due to convergent evolution, which produces similar morphological traits in unrelated groups.

Modern taxonomy

To overcome the issue with similar and cryptic morphologies, in modern times, integrative taxonomy has emerged as a large field and is put forward as the most promising approach to confidently make robust species hypothesis and classifications. Here, one is combining morphological, molecular, ecological and geographic data to produce species hypothesis and classifications, and genomic data ideally complements, rather than replaces, careful morphological and ecological studies. Molecular phylogenies, which are graphical (tree) representations of species relationships based on genomic data, is often helpful and complementary to taxonomic placement of species.

Molecular data, or genomic data, involves DNA and analyses of DNA at varying scale (single markers to whole genomes) and has become the foundation for modern, integrative taxonomy and also phylogenetic research. The goal of integrating genetic data in taxonomy, is to reveal evolutionary processes behind observed diversity.

Genetic data can (to mention some):

• Resolve recent divergences and closely related lineages that morphology cannot distinguish.
• Provide genome-wide markers that reveal subtle structure and fixed differences informative for delimiting species.
• Offer quantitative measures (e.g., genetic distances, allele frequencies, gene-flow estimates) that support formal statistical tests of delimitation and demographic history.

However, using genetic data is powerful, but not flawless. There are still some limitations also with this data. Challenges include incomplete lineage sorting, introgression, horizontal gene transfer and the limits of single-locus markers. For example, mitochondrial DNA barcodes (COI) are useful for rapid identification but reflect only maternal ancestry and may be affected by mitochondrial capture (you can read more about mt genomes here). Practical constraints (cost, lab infrastructure, degraded DNA in old specimens) and the need for bioinformatics skills also matter.

This said, genomics has revolutionized taxonomy, and molecular phylogenies are often the foundation for setting species boundaries and classifying species into ranks in today’s research. This is mostly due to the availability and easy access to genetic data. DNA extraction and sequencing has become both fast, easy and cheap, and biologist today are becoming more and more trained in bioinformatics. However, traditional taxonomical work and traditional taxonomic expertise remains essential for robust species descriptions, nomenclatural stability and biological interpretation, and must not be neglected.

References

Engel, M. S., Ceríaco, L. M. P., Daniel, G. M., Dellapé, P. M., Löbl, I., Marinov, M., . . . Zacharie, C. K. (2021). The taxonomic impediment: a shortage of taxonomists, not the lack of technical approaches. Zoological Journal of the Linnean Society, 193(2), 381-387. 10.1093/zoolinnean/zlab072

Godfray, H. C. J. (2002). Challenges for taxonomy. Nature, 417(6884), 17-19. 10.1038/417017a

Struck, T. H., Feder, J. L., Bendiksby, M., Birkeland, S., Cerca, J., Gusarov, V. I., . . . Dimitrov, D. (2018). Finding Evolutionary Processes Hidden in Cryptic Species. Trends in Ecology & Evolution, 33(3), 153-163. 10.1016/j.tree.2017.11.007