The modern science of biology and genetics arises from a growing understanding about the diversity of life on Earth. The first biologists were those people who sought to organize life into meaningful groups. This is the process of classification – or to give it its more scientific name, ‘taxonomy’.
In the modern context, the work of taxonomists is often seen as the less exciting end of the biological sciences, a labyrinthine field associated with the minutiae of anatomy and lugubrious Latin names. So far taxonomists have classified around 1 million species, and the best estimates suggest this is barely 10 per cent of those living on our planet today. The modern field has changed beyond all recognition from the days when taxonomy was concerned with making drawings of specimens and giving them obscure names. Today, it is as much about tracing the ancestry of organisms throughout natural history as it is about parcelling up life into ever more groups.
The founding figure of taxonomy is Carl von Linné (1707–78), a Swede better remembered by his Latinized name, Linnaeus. However, Linné was by no means the first to attempt to organize life according to a set of rules. Aristotle was one famous forebear though he made many blunders, for example in assuming whales were a kind of fish (the word ‘dolphin’ means ‘womb fish’ in Greek). Aristotle’s mistake was to group organisms according to their habitat and lifestyle alone.
Linnaeus corrected the whale–fish error (eventually) in his Systema Naturae, a method of classification he refined through the mid-18th century. The Linnaean system was based on anatomical features, grouping organisms in a series of ranked groups according to the number of shared features. Linnaeus’ finished list contained around 10,000 organisms, 60 per cent of which were plants (he was a keen gardener). Many aspects of the Systema Naturae persist in modern taxonomy although the classifications have been greatly extended and revised.
Linnaeus took on a Latinized version of his own name because Latin was the lingua franca of European scientists at the time. Every great work was written in Latin to overcome the language barriers and allow knowledge to disseminate better. So it is little wonder that Linnaeus also chose Latin and Greek as the languages for giving official names to the organisms classified in his Systema Naturae. The tradition has stuck to this day because it removes all ambiguities.
Crucially, Linnaeus opted for a binomial system, giving every organism two names. So the animal known in English as a lion is Panthera leo – only the first name is capitalized, and both are italicized. Panthera is the generic name, while leo is the specific one. The generic name refers to the genus to which the lion belongs, shared with similar animals, such as Panthera tigris (the tiger), P. pardus (the leopard) and the other ‘big cats’. The specific name is there to delineate the lions from other big cats.
A species is the end result of the classification system. It denotes a group of organisms that share a large number of physical characteristics. One might think that members of a species always share more features with each other than they do with other members of their genus, and in the great majority of cases that is true – but not always. The crucial factor defining a species is that its members are all able to breed with each other, producing viable offspring that are fertile themselves.
This fact becomes important when considering ‘cryptic species’. These are two populations of animals – often birds or bats – that are effectively indistinguishable by examining anatomy alone, but do not interbreed, and are therefore two distinct species despite looking more or less the same. Taxonomy can also classify organisms to a level lower than species. Many species are made up of subspecies – populations from different regions that may have significant anatomical differences – but are nevertheless able to breed with each other.
Species and genus are examples of taxa (singular: taxon) – a word that derives from the Greek for ‘arrangement’. The classification system puts every organism in a species, members of which share a small gene pool. Species are then placed within a series of increasingly larger taxa, which share larger gene pools. Each species belongs to a genus (plural: genera) and every genus has at least one species. The system continues by organizing genera into families. For example, Panthera, the big cat genus, belongs to Felidae, the cat family. Note that above the genus level, taxa are no longer required to be italicized.
The next taxon is the order. The Felidae belong to an order called Carnivora, alongside the Canidae (dog family), Ursidae (bear family) and other predatory animals. The Carnivora is one of the orders in the class Mammalia – the mammals. In turn, Mammalia is a member of the phylum Chordata, which includes other vertebrates such as reptiles, birds and fish. In botanical classification, the term phylum (plural: phyla) is generally replaced with the term ‘division’.
At first glance, the classification system used today seems to follow the same methods developed by Linnaeus back in the 1750s. It retains the binomial names and the ranks of taxa. However, in the 20th century a new way of organizing life within the system began to dominate. This is cladistics, where species are classified not simply by the way they look and compare to each other, but how they are related by evolution. Every group of organisms that share a common ancestor is called a clade.
Cladistics requires that extinct species be included in the system along with the extant ones. When DNA is not available, taxonomists use statistical analysis of anatomy to find the most likely relationships between organisms, although the classifications produced this way are frequently challenged and changed. A good example of the implications of cladistics is the analysis of reptiles: natural history tells us that mammals and birds all evolved from the same ancestor as reptiles, and accordingly they all belong in the same clade: the Amniota.
One of the aims of classification is to create a big picture of life on Earth. Linnaeus did this using a final, top-ranked taxon called the kingdom. According to him, all life belonged to either the animal kingdom or the plant kingdom. The discovery of microscopic single-celled organisms created a problem: were they tiny animals or plants, or something else? Fungi were subsequently also split from plants, and the number of kingdoms went up. The simplest system used five: Animalia, Plantae, Fungi, Protista (amoebae, etc), and Bacteria. Then in 1977, DNA analysis showed that many cells that looked like bacteria were in fact a completely different set of organisms, now known as the Archaea.
Further analysis showed that the growing number of kingdoms could be grouped into three larger groups called ‘domains’. Bacteria and Archaea occupy one domain each, while all other life lies within the Eukaryota – organisms with complex cells that use organelles (see here).
This diagram shows the proportion of life that lives in each domain. The kingdoms of plants, animals and fungi comprise just three branches.
The only illustration in Darwin’s On the Origin of Species is a branching diagram that shows how evolution by natural selection causes new species to radiate out from a common ancestor. Darwin visualized it more as a creeper or tangle of bushes growing on a steep bank, but the concept has subsequently become known as the ‘Tree of Life’. It is still one of the best ways to visualize the great sweep of biodiversity that natural selection has created.
The trunk of the tree represents the primordial organism from which all life evolved. The trunk then branches into three domains, and each domain splits into kingdoms, phyla and so on. All the plants and animals fill just a third of the tree, and the mammals are represented as a mere sprig. Extant species form the tips of each branch, with the distances between them showing how closely related they are. Meanwhile, branches and twigs represent the intermediate, now-extinct forms they took as they evolved and split away from a common ancestor.
The simple tree diagram that showed Darwin’s thinking as he formulated his theory of evolution.
The fossil record of extinct organisms is far from complete, and the search continues to find specimens that might be common ancestors. However, genome analysis offers an alternative method for discovering when modern organisms shared an ancestor – the so-called ‘molecular clock.’
Every species has a unique genome, at its most basic a long string of ACTG lettering (see here). The molecular clock system compares the differences in the letters between one species and the next. This is possible because while nuclear DNA is changed radically by recombination in every generation, the DNA in a cell’s mitochondria is inherited directly from the organism’s mother. Changes only occur as mutations, appearing at a more or less constant rate, like the ticking of a clock. Thus, there are fewer differences between closely related species than more distantly related ones, and the difference between mitochondrial genomes can be used to estimate when in the past the species diverged from their common ancestor.
The accumulated differences in the genetic code of two organisms, arising from random mutations, provide an indication of the point of time in the past when the two species diverged.