15.1: Systems of Classification

The science of systematics aims to discover the diversity of organisms and their relationships with each other (e.g., Raven et al. 2020). As Narendran (2000) expresses it, “Systematics is nothing less than a thorough and complete study of the diversity of living forms.” Not only is systematics useful for understanding the evolution and history of life, it also provides a kind of biological parts list for the Earth system. Knowing who’s who—differentiating one species from another—helps scientists determine who is doing what and where and when they are doing it (Yilmaz et al. 2016). Discovery of abundant cyanobacteria in the 1970s completely changed our ideas about oceanic food webs. Had we not known these organisms existed, our ideas would have been incomplete, if not fundamentally wrong. Systematics has enabled oceanographers to piece together the microbial machinery that underpins how the ocean works as a system.

Systematics proceeds in part through classification, the organization of life into groups that share certain characteristics. Most of us regularly classify things. For example, when you sort laundry, you separate clothes by color or material. When you put away dishes, you typically place glassware, silverware, and plates in specific locations.

Scientific classification involves the naming of things, a science called taxonomy (e.g., Raven et al. 2020). Traditional rank-based taxonomy, or Linnaean taxonomy, popularized by Swedish naturalist Carl Linnaeus (1707–1778), categorizes life into a series of ever-larger groups from most similar to least similar. The domain category represents the largest grouping of organisms. Wholly related organisms, individuals that share near-identical genetic codes and can produce fertile offspring with each other, are called species. Every species of organism on Earth receives a standardized name—a scientific name—that connects it with its closest relatives—the next highest level of organization, the genus. Scientific names follow binomial nomenclature, a two-part naming system that includes the genus as the first part of the name and the species as the second part. Scientific names also follow strict formatting guidelines: the genus is always capitalized, and both the genus and species are italicized. For example, the properly formatted genus and species for humans appears as Homo sapiens. Additional information may appear as part of a scientific name, but that’s beyond our discussion here.

Higher levels of organization provide additional information on the relatedness of species (see below). Because each of these groupings represents a kind of rank—domains are the highest level of classification—the rank-based system is called a hierarchical system, a system ordered by different levels. The military, with its ranks of personnel, and traditional corporations, with CEOs and managers, use hierarchical systems. However, unlike the military and corporate hierarchies, rank-based taxonomy doesn’t necessarily imply levels of importance in the same way (but see Wilcox 2019). There are no generals in Linnaean taxonomy. In this sense, rank-based taxonomy is a nested hierarchy, like the Russian matryoshka, or nesting dolls—where one rank fits within another.

Rank-based classification helps organize living things into intuitive categories—what biologists refer to as “natural kinds” (e.g., Doolittle 2014). But this system has drawbacks for exploring the evolutionary relationships of organisms, such as who evolved from whom. And it can give a false sense of equivalency between ranks. For example, whereas we find about 89 species of cetaceans (i.e., whales, dolphins, and porpoises) on Earth (Fordyce and Perrin 2023), marine mollusks (i.e., bivalves, shells, octopuses, squids) number in the vicinity of 50–55,000 species (Molluscabase 2023). Mollusks have also lived on Earth about 500 million years longer than cetaceans, having evolved 550 million years ago (e.g., Wanninger and Wollesen 2018) versus 50–53 million years ago for cetaceans (e.g., Bajpai and Gingerich 1998; Thewissen et al. 2007). Though species occupy the same rank, they represent very different evolutionary histories (Understanding Evolution 2023).

With a desire for a more objective and quantitative means of classification, German zoologist Willi Hennig (1913–1976) developed phylogenetic systematics, also known as cladistics (e.g., Lipscomb 1998), a method of classification that uses measurable characteristics to determine degrees of similarity between organisms (Oxford Languages 2023). Cladistics excels at determining who is descended from whom in a more quantitative way than traditional classification. We won’t delve into the details, but a couple terms prove useful for discussing classification based on cladistics. Organisms that share a common ancestor belong to a group called a clade. By definition, a clade includes all members descended from the common ancestor. A group that contains all descendants from a common ancestor is said to be monophyletic. Ideally, all classification would be based on monophyletic clades. But this is easier said than done.

In many instances, a paraphyletic classification—a clade that doesn’t include all descendants from a common ancestor—is desirable. For example, birds and dinosaurs had been traditionally considered separate groups. As it turns out, however, based on discoveries of feather-adorned dinosaurs in China, scientists now believe that birds and dinosaurs share a common ancestor (e.g., Bhullar et al. 2012; Singer 2015). A long history of distinction between birds and reptiles makes it unlikely that we’ll lump birds in with reptiles anytime soon. And there’s practical reasons to maintain separate classifications: birds do different things than reptiles. Ecologically, the two groups are distinct. Thus, because it doesn’t include all descendants from a common ancestor, the clade “dinosaurs” (or non-avian dinosaurs) is paraphyletic. Similarly, the clade “birds” is paraphyletic (because it doesn’t include dinosaurs). Arizona State University’s Dr. Biology (2017) offers this distinction: if you used phylogenetic classification for storing peanut-derived products in your pantry, you’d put peanut butter, peanut oil, and Cracker Jacks on the same shelf. But if you wanted a more functional system, you’d probably separate these items and group them according to how you use them: peanut butter for sandwiches, peanut oil for cooking, and Cracker Jacks for snacks.

Both rank-based classifications and cladistics can be used to construct phylogenetic trees, also known as trees of life. These branching diagrams illustrate the hypothetical evolutionary relationships between organisms. They’re like a family tree that shows your ancestors and relatives, except in this case, the relatives and ancestors are different species. Phylogenetic trees depict the evolutionary history of a clade of organisms (or all organisms; see below) based on their inherited characters—the traits of organisms coded in genes passed down by their ancestors. Choosing different characters can yield different trees. Much of the research on the evolution of life on Earth concerns finding the characters that yield the simplest or most statistically likely tree.

Though many types of trees exist, two types are most common: (1) rooted, like a tree with a main trunk and branches; and (2) unrooted, which resembles a starburst pattern. Rooted trees provide a road map of the ancestry of organisms and their evolution from a common ancestor. Unrooted trees illustrate the relationships between organisms without regard to a common ancestor. A three-branch tree—representing the three domains of life—is perhaps the most common (e.g., Woese et al. 1990). Ever smaller and more numerous branches represent groupings based on more specific characteristics and genomes. (See Understanding Evolution for more details on different types of trees and their uses.)

Of course, without time travel or photos provided by extraterrestrials who visited Earth billions of years ago, we can never be absolutely certain who evolved from whom. That’s why phylogenetic trees are considered hypothetical. Nevertheless, they offer enormous insights into the evolution of life and ecosystems on our planet. They are a fundamental tool for modern biology and ecology.