The Science Decoder

How are species defined? What does it mean for two species to be closely related? Are some organisms really more or less ‘complex’ than others? These are all critically important questions in the field of evolutionary biology, and in order to answer them, we must understand the principles of taxonomy–the study of classifying and understanding the relationships between organisms.

History of Taxonomy

The roots of taxonomic classification can be traced back to the Ancient Greeks in the 4th century BCE. Aristotle, an early philosopher and scientist, developed one of the first influential systems aimed at characterizing organisms. He divided animals into two categories: those that were ‘blooded’ (such as birds, fish, mammals, etc.), and bloodless animals (insects, crustaceans, and other ‘lower’ animals). From this primary division, Aristotle further split animals into more specific categories.¹

This system laid the groundwork for taxonomic classification, but was still fairly limited, as it was heavily influenced by subjective and cultural biases. Aristotle believed that all things could be ranked based on how basic or complex they are, forming the Great Chain of Being, or Scala Naturae in Latin.²

In this system, the lowest entities are abiotic (nonliving) things, such as minerals. Higher than abiotic things are plants, followed by animals–all ranked by how complex Aristotle believed them to be. At the height of this chain are celestial bodies, surpassed only by the First Mover, which Aristotle described as the primary, original force of change and motion in the universe.³

In the mid-18th century, a Swedish botanist named Carolus Linnaeus built upon these ideas by developing a new hierarchical taxonomic system. Linnaean taxonomy introduced binomial nomenclature; binomial, meaning two terms, and nomenclature, meaning the assignment of names.⁵ The first term of any name using binomial nomenclature describes an organism’s genus, and the second term is called the specific epithet. Taken together, these two terms describe an individual species.

For example, humans are Homo sapiens; Homo, meaning ‘man,’ is a genus of large-brained great apes, and sapiens, meaning ‘wise’ or ‘thinking.’ Interestingly, there used to be several other species in the Homo genus, but we are the only ones remaining.⁶

In 1735, Linnaeus published his Systema Naturae–a scientific work which introduced these concepts of biological organization, and essentially birthed the field of modern taxonomy. The Systema Naturae outlined animal species, genera, orders, and classes. He also published the Species Plantarum, which sought to do the same for species of plants.⁵

Although these works were revolutionary, Linnaeus’ understanding of taxonomy was also incomplete, as he believed species were fixed and unchanging, causing him to lack insight into evolutionary relationships.⁵ This system utilizes morphological characteristics to classify organisms, which has at least been partially overshadowed by the popularization of molecular techniques.

We will discuss additional ways that our understanding of taxonomy has changed over time, but first, let’s explain some of these very important concepts introduced by Linnaeus.

What is Linnaean Taxonomy?

With Linnaeus’ seminal work, the field of modern taxonomy was born. Linnaean classification operates as a nested hierarchy; to understand what this means, let’s step away from biology, and into a vending machine.

Imagine that you have a cup in front of you containing an unknown fluid. By looking, smelling, and tasting, you determine it is root beer. With this information, you can place it into nested categories: beverage → flavored drink → carbonated → sweetened → herb/root flavored.

Though it may be a silly way to conceive of taxonomy, Linnaeus’ system is also based on similar broad to specific nested ranking. In Linnaean taxonomy, the highest and most general of these categories is called a domain (not a type of fluid, like in our example), and there are three of them: Archaea, Bacteria, and Eukarya.

You have almost certainly heard of Bacteria, but what are Archaea and Eukarya? 

Simply put, Archaea are unicellular organisms that are thought to be some of the most ancient forms of life on Earth. In fact, archae is the Latin word for primitive/old, which is where this domain gets its name from. Interestingly, many species of Archaea live in extreme conditions, such as in hot springs, exceptionally salty or acidic environments, and even at the bottom of the ocean.⁸

Eukarya are, well, you! Eukaryotic cells have an internal cytoskeleton, and nuclear membranes separating chromosomal DNA from the rest of the cell. Many people think that eukaryotic organisms are all multicellular, but there are single-celled eukaryotes too.⁹

The next level of taxonomy are kingdoms. This is probably a level of organization that you are more familiar with; some examples of the kingdoms within the domain Eukarya include Animalia (animals), Plantae (plants), and Fungi (like mushrooms). Organisms get sorted into kingdoms based on fundamental biological traits, such as mode of reproduction, cell structure, mechanism of nutrition, etc.

The next most specific taxonomic level is the phylum. Some of the phyla with the greatest number of known species are the arthropods and mollusks, both from the kingdom Animalia.

Phyla are made up of classes, which are groups containing species that are even more closely evolutionarily related and physically similar. For example, phylum Arthropoda contains the classes Insecta, Crustacea, and Arachnida.

The taxonomic rank immediately below classes are orders. Within class Insecta are the orders Coleoptera (beetles), Lepidoptera (butterflies and moths), Diptera (flies and mosquitoes), and many more! The insects in these different orders differ slightly in morphological characteristics such as body structures, lifecycle timing, and feeding mechanisms, so they are split up accordingly.

The next taxonomic rung is made up of families. Families share a more recent common ancestor, and even more morphological and genetic similarities. For example, the order Diptera includes families Culicidae (mosquitoes) and Muscidae (house flies).

Families contain genera, such as the genus Culex within the Culicidae family. Finally, genera contain species. Culex bahamensis is a species of mosquito that can be found in the United States, and is a member of the Culex genus.

What’s the Deal With Phylogenetics?

Remember those limitations that we briefly discussed? Linnaean taxonomy classifies organisms based on shared traits, but does not take into account the ancestry of species.

Let’s go back to our beverage example. Although it may be useful to understand aesthetic characteristics about a drink, such as flavor and color, two drinks might look or taste very similar while having wildly different histories or ingredients.

Phylogenetics focuses instead on evolutionary history and ancestry. Imagine for a moment that “proto-root beer” is the ancestral drink which eventually gave rise to modern day root beer. Adding sassafras led to root beer, but adding vanilla and cream led to cream soda. Of course, this is not reflective of the actual history of how these drinks came to be, but it helps to simplify our discussion.

Assuming that the two daughter beverages do not spin off into any other types of drinks, we would say that these three beverages are within the same clade–a group containing the shared common ancestor and all of its descendants.¹⁰

Phylogenetics is the study of evolutionary relationships, and utilizes morphological, behavioral, and genetic data to characterize organisms. Scientists utilize cladistics to construct phylogenetic trees, like the one shown above.¹¹

This focus on ancestry allows for a more accurate understanding of how closely related distinct species are in a way that purely morphological taxonomy cannot. For example, birds (aves) were classified separately from reptiles in the Linnaean system, placed in class Aves and phylum Chordata. Although the birds of today’s world look totally different from most of the dinosaurs we can think of, birds actually evolved from dinosaurs, which makes them reptiles.¹²

Biology can be exceedingly complex, and our assumptions are constantly being challenged by the new things we learn each day. As you have read, there have been several models and methods for developing taxonomic classification to explain the world around us. We have been building the field of taxonomy for millennia, and still we struggle to come up with unified concepts for defining basic terms, such as what species are. This is the struggle and beauty of science, and the job of a scientist is never truly finished.

Thank you for joining us in decoding the principles of taxonomy!

Sources

(1) Biology – Aristotle, Organisms, Cells | Britannica. https://www.britannica.com/science/biology/Aristotelian-concepts (accessed 2025-06-19)

(2) Aristotle: Biology | Internet Encyclopedia of Philosophy. https://iep.utm.edu/aristotle-biology/ (accessed 2025-06-19). 

(3) Great Chain of Being – New World Encyclopedia. https://www.newworldencyclopedia.org/entry/Great_Chain_of_Being (accessed 2025-07-06). 

(4) Great Chain of Being. Encyclopedia Virginia. https://encyclopediavirginia.org/great-chain-of-being/ (accessed 2025-08-06). 

(5) Paterlini, M. There Shall Be Order. The Legacy of Linnaeus in the Age of Molecular Biology. EMBO Rep. 2007, 8 (9), 814–816. https://doi.org/10.1038/sj.embor.7401061. 

(6) Dunsworth, H. M. Origin of the Genus Homo. Evol. Educ. Outreach 2010, 3 (3), 353–366. https://doi.org/10.1007/s12052-010-0247-8. 

(7) mw-parser-output .commons-creator-table{background-color:#f0f0ff;box-sizing:border-box;font-size:95%;text-align:start;color:inherit}.mw-parser-output .commons-creator-table>tbody>tr{vertical-align:top}.mw-parser-output .commons-creator-table>tbody>tr>th{background-color:var. Portrait of Carl von Linné (Carolus Linnaeus)Label QS:Len,”Portrait of Carl von Linné (Carolus Linnaeus)”; 1774. https://commons.wikimedia.org/wiki/File:Carolus_Linnaeus.jpg (accessed 2025-06-19)

(8) Reed, C. J.; Lewis, H.; Trejo, E.; Winston, V.; Evilia, C. Protein Adaptations in Archaeal Extremophiles. Archaea 2013, 2013, 373275. https://doi.org/10.1155/2013/373275. 

(9) Domains of Life, Genomics | Learn Science at Scitable. https://www.nature.com/scitable/topicpage/the-two-empires-and-three-domains-of-14432998/ (accessed 2025-06-19)

(10) clade. https://evolution.berkeley.edu/glossary/clade/ (accessed 2025-08-12)

(11) Reconstructing trees: Cladistics. https://evolution.berkeley.edu/phylogenetic-systematics/reconstructing-trees-cladistics/ (accessed 2025-08-17). 

(12) Are Birds Reptiles? https://www.petmd.com/bird/are-birds-reptiles (accessed 2025-08-14).