Taxonomy 1: Principles of Biological Classification
Learning Objectives
- Explain the role of taxonomy in the classification, identification, and naming of living organisms
- Describe the hierarchical classification system from domain to species and apply the principles of binomial nomenclature
- Compare morphological, genetic, and evolutionary evidence used to classify organisms and determine biological relationships
- Differentiate between homologous and analogous structures and explain their importance in evolutionary biology
- Interpret phylogenetic trees and clades to evaluate patterns of common ancestry and evolutionary divergence
- Describe the evolutionary classification of humans and explain the traits that distinguish primates, hominids, and modern humans
Taxonomy
Taxonomy is the classification, description, identification, and naming of living organisms. Classification is the practice of organising organisms into different groups based on their shared characteristics.Taxonomy (which literally means “arrangement law”) is the science of naming and grouping species to construct an internationally shared classification system. The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish naturalist) uses a hierarchical model. A hierarchical system has levels and each group at one of the levels includes groups at the next lowest level, so that at the lowest level each member belongs to a series of nested groups.
Carl Linnaeus
The most famous early taxonomist was a Swedish botanist, zoologist, and physician named Carolus Linnaeus (1701–1778). In 1735, Linnaeus published Systema Naturae, an 11-page booklet in which he proposed the Linnaean taxonomy, a system of categorising and naming organisms using a standard format so scientists could discuss organisms using consistent terminology. He continued to revise and add to the book, which grew into multiple volumes (Figure 3.2).
In his taxonomy, Linnaeus divided the natural world into three kingdoms: animal, plant, and mineral (the mineral kingdom was later abandoned). Within the animal and plant kingdoms, he grouped organisms using a hierarchy of increasingly specific levels and sublevels based on their similarities. The names of the levels in Linnaeus’s original taxonomy were kingdom, class, order, family, genus (plural: genera), and species. Species was, and continues to be, the most specific and basic taxonomic unit.
Levels of classification
Linnaeus published his classification system in the 1700s. Since then, many new species have been discovered. Scientists can also now classify organisms based on their biochemical and genetic similarities and differences rather than just their outward morphology. These changes have led to revisions in the original Linnaean system of classification.A major change to the Linnaean system is the addition of a new taxon called the domain. The domain is a taxon that is larger and more inclusive than the kingdom).
Scientists divide organisms into three domains: Bacteria, Archaea, and Eukarya (Figure 3.3). Both the Bacteria and the Archaea domains consist of single-celled organisms that lack a nucleus. This means that their genetic material is not enclosed within a membrane inside the cell. The Eukarya domain, in contrast, consists of all organisms whose cells have a nucleus. In other words, their genetic material is enclosed within a membrane inside the cell. The Eukarya domain is made up of both single-celled and multicellular organisms. This domain includes several kingdoms, including the animal, plant, fungus, and protist kingdoms.
Within each domain is a second level called a kingdom. Bacteria and Archaea each only have one kingdom, while Eukarya contains several. Within kingdoms, the subsequent categories of increasing specificity include phylum, class, order, family, genus, and species. The phylum category groups organisms based on shared fundamental physical body plans or common significant structural features. The organisms within the same phylum tend to have common ancestry and share developmental patterns. The class category groups organisms that share a higher level of similarities, often focusing on reproductive methods and detailed structural features. The next category, order, groups organisms that share similarities in physical characteristics, evolutionary traits, and unique adaptations or behaviours. The family category groups the genera (plural of genus) that share high levels of characteristic similarities what are both structurally and evolutionarily closely related.
The classification levels can be seen in the example of the domestic dog (Figure 3.4). The group at each level is called a taxon (plural: taxa). In other words, for the dog, Carnivora is the taxon at the order level, Canidae is the taxon at the family level, and so forth. Organisms also have a common name that people typically use, such as domestic dog, or wolf. Each taxon name is capitalised except for species, and the genus and species names are italicised. Scientists refer to an organism by its genus and species names together, commonly called a scientific name, or Latin name. This two-name system is called binomial nomenclature. The scientific name of the wolf is therefore Canis lupus. Recent study of the DNA of domestic dogs and wolves suggest that the domestic dog is a subspecies of the wolf, not its own species, thus it is given an extra name to indicate its subspecies status, Canis lupus familiaris.
Figure 3.4 also shows how taxonomic levels move toward specificity. Notice how within the domain we find the dog grouped with the widest diversity of organisms. These include plants and other organisms not pictured, such as fungi and protists. At each sublevel, the organisms become more similar because they are more closely related. Before Darwin’s theory of evolution was developed, naturalists sometimes classified organisms using arbitrary similarities, but since the theory of evolution was proposed in the 19th century, biologists work to make the classification system reflect evolutionary relationships. This means that all members of a taxon should have a common ancestor and be more closely related to each other than to members of other taxa.
Binomial nomenclature
As noted above, binomial nomenclature is a two-worded naming system for identifying organisms by genus and specific epithet, such as Canis lupus, or Homo sapiens. Taxonomic names in the 18th through 20th centuries were typically derived from Latin, since that was the common language used by scientists when taxonomic systems were first created. Today, newly discovered organisms can be given names derived from Latin, Greek, or English. Sometimes these names reflect some distinctive trait of the organism; in other cases, microorganisms are named after the scientists who discovered them. The archaeon Haloquadratumwalsbyi(commonly known as Walsby’s square bacterium) is an example of both of these naming schemes. The genus, Haloquadratum, describes the microorganism’s saltwater habitat (halo is derived from the Greek word for “salt”) as well as the arrangement of its square cells, which are arranged in square clusters of four cells (quadratum is Latin for “foursquare”). The species, walsbyi, is named after Anthony Edward Walsby, the microbiologist who discovered Haloquadratumwalsbyi in 1980.
It might seem easier to give an organism a common descriptive namebut this can become problematic.The Australian funnel web spider is name for its distinct webbed burrow however, there arealmost 40 distinct species of funnel web spider classified,differing in size, behaviour and toxicity. The systematic nomenclature scientists use eliminatesconfusion by assigning each organism a single, unique two-word name that is recognised by scientists all over the world.This unique naming convention typically abbreviates an organism’s genus and species after its first (full) mention. The abbreviated form is simply the first initial of the genus, followed by a period and the full name of the species. For example, the bacterium Escherichia coli is shortened to E. coli in its abbreviated form. You will encounter this same convention in other scientific texts as well.
Characteristics considered with traditional classification methods
Scientists collect information that allows them to make evolutionary connections between organisms. Similar to detective work, scientists must use evidence to uncover the facts. In the case of phylogeny, evolutionary investigations focus on two types of evidence: morphologic (form and function) and genetic.
Organisms that share similar physical features and genetic sequences tend to be more closely related than those that do not. Features that overlap both morphologically and genetically are referred to as homologous structures, the similarities stem from common evolutionary paths. This is illustrated in comparisons of the bones in the wings of bats and birds, the arms of humans, and the foreleg of a horse being homologous structures (Figure 3.5). Notice the structure is not simply a single bone, but rather a grouping of several bones arranged in a similar way in each organism even though the elements of the structure may have changed shape and size.
Some organisms may be very closely related, even though a minor genetic change caused a major morphological difference to make them look quite different. For example, chimpanzees and humans, the skulls of which are shown in Figure 3.6 are very similar genetically, sharing 99 percent of their genes. However, chimpanzees and humans show considerable anatomical differences, including the degree to which the jaw protrudes in the adult and the relative lengths of our arms and legs.
However, unrelated organisms may be distantly related yet appear very much alike, usually because common adaptations to similar environmental conditions evolved in both. An example is the streamlined body shapes, the shapes of fins and appendages, and the shape of the tails in fishes and whales, which are mammals. These structures bear superficial similarity because they are adaptations to moving and manoeuvring in the same environment—water. When a characteristic that is similar occurs by adaptive convergence (convergent evolution), and not because of a close evolutionary relationship, it is called an analogous structure. In another example, insects use wings to fly like bats and birds. We call them both wings because they perform the same function and have a superficially similar form, but the embryonic origin of the two wings is completely different. The difference in the development, or embryogenesis, of the wings in each case is a signal that insects and bats or birds do not share a common ancestor that had a wing. The wing structures, shown in Figure 3.7 evolved independently in the two lineages.
Similar traits can be either homologous or analogous. Homologous traits share an evolutionary path that led to the development of that trait, and analogous traits do not. Scientists must determine which type of similarity a feature exhibits to decipher the phylogeny of the organisms being studied.
Phylogeny
With advances in technology, other scientists gradually made refinements to the Linnaean system and eventually created new systems for classifying organisms. In the 1800s, there was a growing interest in developing taxonomies that took into account the evolutionary relationships, or phylogenies, of all different species of organisms on earth. One way to depict these relationships is via a diagram called a phylogenetic tree (or tree of life). In these diagrams, groups of organisms are arranged by how closely related they are thought to be. Phylogenetic trees serve to show a pictorial example of how organisms are believed to be related evolutionarily. The root of the tree is the last common ancestor for the organisms being compared (Last Universal Common Ancestor or LUCA, if doing a comparison of all living cells on Earth).
Each internal node (or branchpoint) represents an occurrence where the organisms diverged, based on a genetic change in one organism. The length of each branch can indicate the amount of molecular changes over time, if the phylogenetic tree is scaled. The external nodes represent specific taxa or organisms (although they can also represent specific genes). A clade indicates a group of organisms that all have a particular ancestor in common (Figure 3.8).
Linnaeus’s tree of life contained just two main branches for all living things: the animal and plant kingdoms. In 1866, Ernst Haeckel, a German biologist, philosopher, and physician, proposed another kingdom, Protista, for unicellular organisms (Figure 3.9). He later proposed a fourth kingdom, Monera, for unicellular organisms whose cells lack nuclei, like bacteria.
Almost 100 years later, in 1969, American ecologist Robert Whittaker (1920–1980) proposed adding another kingdom—Fungi—in his tree of life. Whittaker’s tree also contained a level of categorisation above the kingdom level—the empire or super kingdom level—to distinguish between organisms that have membrane-bound nuclei in their cells (eukaryotes) and those that do not (prokaryotes). Empire Prokaryota contained just the Kingdom Monera.
The Empire Eukaryota contained the other four kingdoms: Fungi, Protista, Plantae, and Animalia. Whittaker’s five-kingdom tree was considered the standard phylogeny for many years (Figure 3.10).Note that viruses are not found in any of these trees. That is because they are not made up of cells and thus it is difficult to determine where they would fit into a tree of life.
In the 1970s, American microbiologist Carl Woese discovered what appeared to be a “living record” of the evolution of organisms. He and his collaborator George Fox created a genetics-based tree of life based on similarities and differences they observed in the gene sequences coding for small subunit ribosomal RNA (rRNA) of different organisms. In the process, they discovered that a certain type of bacteria, called archaebacteria (now known simply as archaea), were significantly different from other bacteria and eukaryotes in terms of their small subunit rRNA gene sequences. To accommodate this difference, they created a tree with three Domains above the level of Kingdom: Archaea, Bacteria, and Eukarya (Figure 3.11). Analysis of small subunit rRNA gene sequences suggests archaea, bacteria, and eukaryotes all evolved from a common ancestral cell type. The tree is skewed to show a closer evolutionary relationship between Archaea and Eukarya than they have to Bacteria.
Human classification in the Animal Kingdom
You probably know that modern humans belong to the species Homo sapiens. But what is our place in nature? How are our species classified? A simple classification is represented in Figure 3.12. Humans can move on their own and are placed in the animal kingdom. Further, humans belong to the animal phylum known as chordates because we have a backbone. The human animal has hair and milk glands, so we are placed in the class of mammals. Within the mammal class, humans are placed in the primate order.
What makes us primates?
Living members of the primate order include monkeys, apes, and humans; and any member of this order of mammals is called a primate. At some point in the distant past, we shared ape-like ancestors with all these modern groups of primates. We share between 93 percent and almost 99 percent of our DNA sequences with them, providing hard evidence that we have relatively recent common ancestors. Besides genes, what traits do we share with other primates? Primates are considered generalists among mammals. A generalist is an organism that can thrive in a wide variety of environmental conditions and make use of a variety of different resources, such as consuming many different types of food. Although primates exhibit a wide range of characteristics, there are several traits that are shared by most primates.
Primates have five digits (fingers or toes) on each extremity (hand or foot). The fingers and toes have nails instead of claws and are covered with sensitive tactile pads. The thumbs (and in many species the big toes as well) are opposable, meaning they can be brought into opposition with the other digits, allowing both a power grasp and a precision grip. You can see these features of the primate extremities in the capuchin monkey (Figure 3.13).
The primate body is generally semi-erect or erect, and primates have one of several modes of locomotion, including walking on all four legs (quadrupedalism), vertical clinging and leaping, swinging from branch to branch in trees (brachiation), or walking on two legs (bipedalism), the last of which applies only to our own species today. The primate shoulder girdle has a collar bone (clavicle), which is associated with a wide range of motion of the upper limbs. Relative to other mammals, primates rely less on their sense of smell. They have a reduced snout and relatively small area in the brain for processing olfactory (odour) information. Primates rely more on their sense of vision, which shows several improvements over that of other mammals. Most primates can see in colour. Primates also tend to have large eyes with forward-facing placement in a relatively flat face. This results in an overlap of the visual fields of the two eyes, allowing stereoscopic vision, or three-dimensional, vision. Other indications of the importance of vision to primates are the protection given to the eyes by a complete bony eye socket and the large size of the occipital lobe of the brain where visual information is processed.
Primates are noted for their relatively large brains, high degree of intelligence, and complex behaviours. The part of the brain that is especially enlarged in primates is the cerebrum, which analyses and synthesises sensory information and transforms it into motor behaviours appropriate to the environment. Primates tend to have longer lifespans than most other mammals. In particular, there is a lengthening of the prenatal period and the postnatal period of dependency of infants on adults, providing an extended opportunity for learning in juveniles. Most primates live in social groups. In fact, primates are among the most social of animals. Depending on the species, adult nonhuman primates may live in mated pairs or in groups of up to hundreds of members.
Arboreal origins and global distribution
Scientists think that many primate traits are adaptations to an arboreal, or tree-dwelling, lifestyle. Primates are thought to have evolved in trees, and the majority of primates still live in trees. For life in the trees, the sense of vision trumps the sense of smell, and three-dimensional vision is especially important for grasping the next branch or limb. Having mobile limbs, a good grip, and manual dexterity are matters of life and death when one lives high above the ground. While some modern primates are mainly terrestrial (ground-dwelling) rather than arboreal, all primates possess adaptations for life in the trees. The present distribution of nonhuman primates around the world is shown in Figure 3.14. Tropical forests in Central and South America are home to many species of monkeys, including the capuchin monkey pictured above. Old World tropical forests in Africa and Asia are home to many other species of monkeys, including the crab-eating macaque pictured above, as well as all modern apes.
The Hominid Family
Who are our closest relatives in the primate order? We are placed in the family called Hominidae. Any member of this family is called a hominid. Hominids include four living genera: chimpanzees, gorillas, orangutans, and humans. Among these four genera are just seven living species: two in each genera except humans, with our sole living species, Homo sapiens. The Orangutan mother (Figure 3.15) cradling her child shows how similar these hominids are to us.
Hominids are relatively large, tailless primates, ranging in size from the bonobo, or pygmy chimpanzee, which may weigh as little as 30 kg (66 lb), to the eastern gorilla, which may weigh over 200 kg (440 lb). Most modern humans fall somewhere in between that range. In all species of hominids, males are somewhat larger and stronger, on average, than females, but the differences may not be great. Except for humans, hominids are mainly quadrupedal, although they can get around bipedally if needed to gather food or nesting materials. Humans are the only habitually bipedal species of living hominids.
Evolution and defining traits of the Genus Homo
Within the hominid family, our species is placed in the genus Homo. Our species, Homo sapiens, is the only living species in this genus. Several earlier species of Homo existed but have since gone extinct, including the species Homo erectus. An artist’s reconstruction of a Homo erectus individual is shown in Figure 3.16.
By about 2.8 million years ago, early Homo species such as Homo erectus were probably nearly as efficient at bipedal locomotion as modern humans. Relative to quadrupedal primates, they had a broader pelvis, longer legs, and arched feet. However, from the neck up, they were still quite different from us. They typically had bigger jaws and teeth, a sloping forehead, and a relatively small brain.
During the roughly 2.8 million years of the evolution of the Homo genus, the remaining features of Homo sapiens evolved. These features include:
- small front teeth (incisors and canines) with relatively large molars, at least compared to other primates.
- a decrease in the size of the jaws and face, and an increase in the size of the cranium, forming a nearly vertical forehead.
- a tremendous enlargement of the brain, especially in the cerebrum, which is the site of higher intellectual functions.
The increase in brain size occurred very rapidly as far as evolutionary change goes, between about 800,000 and 100,000 years ago. During this period, the size of the brain increased from about 600 cm3 to about 1400 cm3 and the earliest Homo sapiens appeared. This was also a period of rapid climate change, and many scientists think that climate change was a major impetus for the evolution of a larger, more complex brain. In this view, as the environment became more unpredictable, bigger, “smarter” brains helped our ancestors survive. Paralleling the biological evolution of the brain was the development of culture and technology as behavioural adaptations for exploiting the environment. These developments, made possible by a big brain, allowed modern humans and their recent ancestors to occupy virtually the entire world and become the dominant land animals.
Our species Homo sapiens is the most recent iteration of the basic primate body plan. Because of our big, complex brain, we clearly have a much greater capacity for abstract thought and technological advances than any other primate, even chimpanzees who are our closest living relatives. However, it is important to recognise that in other ways, we are not as adept as other living hominids around the world. We are physically weaker than gorillas, far less agile than orangutans, and arguably less well-mannered than bonobos.
Real World Application
Studies of human biological variation evaluate the physical similarities and differences between human populations across both time and space. Differences in morphology include features such as height, jawline, eye sockets, and ear and nose shape and size. Biochemical differences account for variations in the sense of smell, mutations in the CCR5 gene that offer resistance to HIV, and variations in skin pigmentation in response to levels of exposure to ultraviolet rays from the sun.
The study of human biological variation is closely linked to the original conception of biological anthropology, which was formalised in 1930 with the establishment of the American Association of Physical Anthropologists, recently renamed the American Association of Biological Anthropologists. The change in name is an effort to move away from the term physical anthropology, which has come to be associated with views promoting scientific racism that no longer represent or align with views held by anthropologists today. In 1951, American anthropologist Sherwood Washburn introduced a “new physical anthropology,” changing the focus from racial typology and classification to the study of human evolution and the evolutionary process. This new focus expanded anthropology as a field to include paleoanthropology and primatology
Paleoanthropology looks at the fossil evidence of humanity’s ancestors along with ancient material culture such as tools and other human artifacts. The physical morphology (shape and size) of skulls and other postcranial material (skeletal remains other than the skull) allow paleoanthropologists to form hypotheses about important milestones in human evolution over time.
Primatology examines the behavioural and physical attributes of both living and fossil primates as well as their relationships with their environments. Humans are primates who share a common ancestry with nonhuman primates. By studying nonhuman primates, anthropologists can gain a better understanding of what it means to be a primate and what it means to be human.
Genetic anthropology is used within several areas of biological anthropology. In this specialised area, DNA testing is combined with archaeological, historical, and linguistic evidence to reveal the history of ancient human migration or to track human disease.
Forensic anthropology is a subfield of biological anthropology that applies scientific methods to the analysis of human remains for the purposes of identifying a victim and determining the possible cause of death. A major difference between forensic anthropology and other types of biological anthropology is that forensic anthropology is usually focused on crime scenes involving the death of an individual, whereas other types primarily focus on understanding patterns and features that may appear in a group or an entire population. Beginning in World War II, forensic anthropologists have been instrumental in helping identify victims of war and disasters. They have played critical roles in identifying victims of the Thailand tsunami in 2004 and the destruction of the World Trade Centre on September 11, 2001. Today, most forensic anthropologists work in a medical examiner’s office, assisting with autopsies and examinations of skeletal remains.
Bioarchaeology studies human remains in archaeological settings with a focus on what skeletal material can reveal about the culture, diet, and presence of disease in a population. Bioarchaeologists are also interested in the socioecological system of a population, which helps anthropologists better understand the roles of environmental and ecological pressures and influences in shaping cultural identity, social inequity, sustainability, and access to and use of resources. Based on the biological remains found at archaeological sites, bioarchaeologists explore questions pertaining to social and funerary behaviour, diet and nutrition, health, and disease. Bioarchaeology offers a window into the connections among biology, society, and culture. An example of what a bioarchaeologist might study is skeletal evidence of infant cranial boarding, which was practiced by many cultures, including the ancient Maya, the Inca, and some Native North American groups. The process involved binding a child’s head to a flat board in order to artificially deform the skull, possibly to meet an aesthetic ideal or to signify social status. Bioarcheologists have found that variations in how the board was attached to the skull provide important information about an individual’s social identity.
Ann Rosalie David
Personal History: Professor Ann Rosalie David was born in Cardiff, UK and earned a bachelor of arts degree in ancient history from University College London in 1967 and a doctorate from the University of Liverpool in 1971. Her thesis was on ancient Egyptian temple rituals.
Area of Anthropology: The focus of Professor’s David’s work has been biological anthropology and Egyptology.
Accomplishments In the Field: Professor David is a Director of the KNH Centre for Biological and Forensic Studies in Egyptology at the University of Manchester. In this role, she established the Ancient Egyptian Mummy Tissue Bank, one of the only such tissue banks in the world. She served as the keeper of Egyptology at the Manchester Museum and has often worked in collaboration with Egypt’s Ministry of Health and Population on public health projects. One such project involved the identification of antibodies against schistosomiasis, a parasite spread by freshwater snails, in Egyptian mummies.
David was made an Officer of the Order of the British Empire (OBE) in 2003 for her work in Egyptology. David has appeared in or consulted on several documentaries, including the television miniseries Private Lives of the Pharaohs (2000) and Secrets of the Pharaohs (2001) and the documentary short Mummies: Secrets of the Pharaohs (2007).
Importance of Her Work: Ann Rosalie David was the first woman in Britain to hold a professorship in Egyptology. She was a pioneer in biomedical research, conducting research on disease, diet, and lifestyles in ancient Egypt. In 2010, her work on ancient Egyptian mummies found evidence to suggest that cancer may be a human-created disease, attributable in part to modern pollution and changes in lifestyle and diet (David and Zimmerman 2010).
The second-highest taxonomic rank beneath domain, commonly dividing life into Bacteria, Archaea, Protista, Fungi, Plantae, and Animalia depending on the taxonomic framework used.
A major taxonomic rank beneath kingdom that groups organisms sharing a fundamental structural body plan and common developmental patterns.
A taxonomic rank beneath phylum that groups organisms based on reproductive methods and more specific anatomical similarities.
A taxonomic category beneath class grouping families that share specific behavioral adaptations, physical features, and evolutionary paths.
A taxonomic rank beneath order that groups closely related genera showing high structural and evolutionary kinship.
A taxonomic category beneath family that groups species sharing close structural and evolutionary traits; the first, capitalised word in binomial nomenclature.
Anatomical features in different species that share a common ancestral origin and embryonic development, regardless of their current specialised function.
The evolutionary history and developmental pathways of a species or group of related organisms.
Diagrammatic representations that depict the hypothesised evolutionary pathways, nodes of divergence, and genetic relationships among species.
The hypothetical primitive, ancestral cell type (LUCA) from which all current cellular life on Earth descended.
A branch point on a phylogenetic tree representing where a single ancestral lineage split into distinct new lineages.
The tips of a phylogenetic tree, representing currently existing taxa, individual organisms, or analysed genes.
A group of organisms on a phylogenetic tree consisting of a common ancestor and all of its descendants; also known as a monophyletic group.
A member of the order of mammals that includes monkeys, apes, and humans, characterised by binocular color vision, manual dexterity, and large brains.
An organism capable of surviving and thriving in a wide variety of environmental conditions and utilising diverse resources.
A member of the primate family Hominidae, which includes chimpanzees, gorillas, orangutans, and humans.
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