Until the late twentieth century, scientists most commonly grouped living things into five kingdoms—animals, plants, fungi, protists, and bacteria—based on several criteria, such as absence or presence of a nucleus and other membrane-bound organelles, absence or presence of cell walls, multicellularity, and mode of nutrition. In the late twentieth century, the pioneering work of Carl Woese and others compared nucleotide sequences of small-subunit ribosomal RNA (SSU rRNA), which resulted in a dramatically different way to group organisms on Earth. Based on differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed that all life on Earth evolved along three lineages, called domains. The three domains are called Bacteria, Archaea, and Eukarya (Fig 14.1).

Two of the three domains—Bacteria and Archaea—are prokaryotic, meaning that they lack both a nucleus and true membrane-bound organelles. However, they are now considered, on the basis of membrane structure and rRNA, to be as different from each other as they are from the third domain, the Eukarya. Prokaryotes were the first inhabitants on Earth, perhaps appearing approximately 3.9 billion years ago. Today they are ubiquitous—inhabiting the harshest environments on the planet, from boiling hot springs to permanently frozen environments in Antarctica, as well as more benign environments such as compost heaps, soils, ocean waters, and the guts of animals (including humans). The Eukarya include the familiar kingdoms of animals, plants, and fungi. They also include a diverse group of kingdoms formerly grouped together as protists.

Prokaryotic Diversity

Prokaryotes were the first forms of life on Earth, and they existed for billions of years before plants and animals appeared. During the first 2 billion years of Earth’s existence, the atmosphere was anoxic, meaning that there was no oxygen. Therefore, the first organisms were anaerobic organisms, meaning their metabolism did not rely on oxygen. Phototrophic organisms that required an organic source of carbon appeared within one billion years of the formation of Earth. Then, cyanobacteria, also known as blue-green algae, evolved from these simple phototrophs one billion years later. Cyanobacteria began the oxygenation of the atmosphere. The increase in oxygen concentration allowed the evolution of other life forms.

Some prokaryotes are able to thrive and grow under conditions that would kill a plant or animal. Bacteria and archaea that grow under extreme conditions are called extremophiles, meaning “lovers of extremes.” Extremophiles have been found in extreme environments of all kinds, including the depths of the oceans, hot springs, the Arctic and the Antarctic, very dry places, deep inside Earth, harsh chemical environments, and high radiation environments. Extremophiles give us a better understanding of prokaryotic diversity and open up the possibility of the discovery of new therapeutic drugs or industrial applications. They have also opened up the possibility of finding life in other places in the solar system, which have harsher environments than those typically found on Earth. Many of these extremophiles cannot survive in moderate environments.

Biofilms

Until a couple of decades ago, microbiologists thought of prokaryotes as isolated entities living apart. This model, however, does not reflect the true ecology of prokaryotes, most of which prefer to live in communities where they can interact. A biofilm is a microbial community held together in a gummy-textured matrix, consisting primarily of polysaccharides secreted by the organisms, together with some proteins and nucleic acids. Biofilms grow attached to surfaces. Some of the best-studied biofilms are composed of prokaryotes, although fungal biofilms have also been described.

Biofilms are present almost everywhere. They cause the clogging of pipes and readily colonize surfaces in industrial settings. They have played roles in recent, large-scale outbreaks of bacterial contamination of food. Biofilms also colonize household surfaces, such as kitchen counters, cutting boards, sinks, and toilets.

Interactions among the organisms that populate a biofilm, together with their protective environment, make these communities more robust than are free-living, or planktonic, prokaryotes. Overall, biofilms are very difficult to destroy, because they are resistant to many of the common forms of sterilization.

Characteristics of Prokaryotes

There are many differences between prokaryotic and eukaryotic cells. However, all cells have four common structures: a plasma membrane that functions as a barrier for the cell and separates the cell from its environment; cytoplasm, a jelly-like substance inside the cell; genetic material (DNA and RNA); and ribosomes, where protein synthesis takes place. Prokaryotes come in various shapes, but many fall into three categories: cocci (spherical), bacilli (rod-shaped), and spirilla (spiral-shaped) (Fig 14.2).

Prokaryotes are unicellular organisms that lack organelles surrounded by membranes. Therefore, they do not have a nucleus but instead have a single chromosome—a piece of circular DNA located in an area of the cell called the nucleoid. Most prokaryotes have a cell wall lying outside the plasma membrane. The composition of the cell wall differs significantly between the domains Bacteria and Archaea (and their cell walls also differ from the eukaryotic cell walls found in plants and fungi.) The cell wall functions as a protective layer and is responsible for the organism’s shape. Some other structures are present in some prokaryotic species, but not in others. For example, the capsule found in some species enables the organism to attach to surfaces and protects it from dehydration. Some species may also have flagella (singular, flagellum) used for locomotion, and pili (singular, pilus) used for attachment to surfaces and to other bacteria for conjugation. Plasmids, which consist of small, circular pieces of DNA outside of the main chromosome, are also present in many species of bacteria.

Both Bacteria and Archaea are types of prokaryotic cells. They differ in the lipid composition of their cell membranes and in the characteristics of their cell walls. Both types of prokaryotes have the same basic structures, but these are built from different chemical components that are evidence of an ancient separation of their lineages. The archaeal plasma membrane is chemically different from the bacterial membrane; some archaeal membranes are lipid monolayers instead of phosopholipid bilayers.

Gram-positive and Gram-negative Bacteria

Bacterial cell walls contain peptidoglycan, composed of polysaccharide chains cross-linked to peptides. Bacteria are divided into two major groups: Gram-positive and Gram-negative, based on their reaction to a procedure called Gram staining. The different bacterial responses to the staining procedure are caused by cell wall structure. Gram-positive organisms have a thick wall consisting of many layers of peptidoglycan. Gram-negative bacteria have a thinner cell wall composed of a few layers of peptidoglycan and additional structures, surrounded by an outer membrane (Fig 14.3).

Eukaryotic Diversity

Living eukaryotes are all descendants of a single common ancestor. Mapping the characteristics found in all major groups of eukaryotes reveals that the following characteristics are present in at least some of the members of each major lineage, or during some part of their life cycle, and therefore must have been present in the last common ancestor.

1. Nuclei surrounded by a nuclear envelope: This is the single characteristic that is both necessary and sufficient to define an organism as a eukaryote. All extant eukaryotes have cells with nuclei.
2. Mitochondria: Most extant eukaryotes have “typical” mitochondria, although some eukaryotes have very reduced mitochondrial “remnants” and a few lack detectable mitochondria.
3. Cytoskeleton of microtubules and microfilaments: Eukaryotic cells possess the structural and motility components called actin microfilaments and microtubules. All extant eukaryotes have these cytoskeletal elements.
4. Flagella and cilia: Organelles associated with cell motility. Some extant eukaryotes lack flagella and/or cilia, but their presence in related lineages suggests that they are descended from ancestors that possessed these organelles.
5. Histone proteins organize chromosomes: Each eukaryotic chromosome consists of a linear DNA molecule coiled around proteins called histones. The few eukaryotes with chromosomes lacking histones clearly evolved from ancestors that had them.
6. Mitosis: A process of nuclear division in which replicated chromosomes are divided and separated using elements of the cytoskeleton. Mitosis is universally present in eukaryotes.
7. Sexual reproduction: A meiotic process of nuclear division and genetic recombination unique to eukaryotes. During this process, diploid nuclei at one stage of the life cycle undergo meiosis to yield haploid nuclei, which subsequently fuse together to create a diploid zygote nucleus.

all extant eukaryotes are likely the descendants of a chimera-like organism that was a composite of a host cell and the cell(s) of an alpha-proteobacterium that “took up residence” inside it. This major theme in the origin of eukaryotes is known as endosymbiosis, one cell engulfing another such that the engulfed cell survives and both cells benefit. Over many generations, a symbiotic relationship can result in two organisms that depend on each other so completely that neither could survive on its own. Endosymbiotic events likely contributed to the origin of the last common ancestor of today’s eukaryotes and to later diversification in certain lineages of eukaryotes. Similar endosymbiotic associations are not uncommon in living eukaryotes.

Plants

Current evolutionary thought holds that all land plants are monophyletic: that is, descendants of a single common ancestor. The evolutionary transition from water to land imposed severe constraints on the ancestors of contemporary plants. Plants had to evolve strategies to avoid drying out, to disperse reproductive cells in air, for structural support, and to filter sunlight. While seed plants developed adaptations that allowed them to populate even the most arid habitats on Earth, full independence from water did not happen in all plants, and most seedless plants still require a moist environment.

Plants are a large and varied group of organisms. There are close to 300,000 species of catalogued plants. Of these, about 260,000 are plants that produce seeds. The plant kingdom contains mostly photosynthetic organisms; a few parasitic forms have lost the ability to photosynthesize. The process of photosynthesis uses chlorophyll, which is located in organelles called chloroplasts. Plants possess cell walls containing cellulose. Most plants reproduce sexually, but they also have diverse methods of asexual reproduction.

Most plants exhibit alternation of generations, which describes a life cycle in which an organism has both haploid and diploid multicellular stages. The haploid multicellular form known as a gametophyte is followed in the development sequence by a multicellular diploid organism, the sporophyte. The gametophyte gives rise to the gametes, or reproductive cells, by mitosis. It can be the most obvious phase of the life cycle of the plant, as in the mosses, or it can occur in a microscopic structure, such as a pollen grain in the higher plants (the collective term for the vascular plants). The sporophyte stage is barely noticeable in lower plants (the collective term for the plant groups of mosses, liverworts, and hornworts). Towering trees are the diplontic phase in the lifecycles of plants such as sequoias and pines.

Charophytes are one of the two groups of green algae and are the closest relatives of land plants. Land plants and the charophytes are part of a monophyletic group called Streptophyta (Table 14.1; Fig 14.4). Land plants (embryopytes) are classified into two major groups according to the absence or presence of vascular tissue (Table 14.1; Fig 14.4). Plants that lack vascular tissue, called the bryophytes, are formed of specialized cells for the transport of water and nutrients. The bryophytes (liverworts, mosses, and hornworts) are seedless and nonvascular, and likely appeared early in land plant evolution. Vascular plants developed a network of cells that conduct water and solutes through the plant body (phloem and xylem). Vascular tissue was an important adaptation that enabled evolution of great diversity of land plants. Vascular plants dominate; they make up over 90% of all land plants. Lycophytes and monilophytes are vascular plants that lack seeds. Seeds are embryos with their stored food reserves protected by a hard casing. The seed-producing plants form the largest group of all existing plants and, hence, dominate the landscape. Seeds and pollen—two adaptations to drought—distinguish seed plants from other (seedless) vascular plants. Seed plants include gymnosperms, most notably conifers, which produce “naked seeds,” and the most successful plants, the angiosperms (also called the flowering plants), which protect their seeds inside chambers at the center of a flower. The walls of these chambers later develop into fruits. Angiosperm success is a result of two novel structures that ensure reproductive success: flowers and fruit. Flowers allowed plants to form cooperative evolutionary relationships with animals, in particular insects, to disperse their pollen to female gametophytes in a highly targeted way. Fruit protect the developing embryo and serve as an agent of dispersal. Angiosperms (flowering plants) are divided into two major groups, according to the structure of the cotyledons, the pollen grains, and other features: monocots, which include grasses and lilies, and eudicots or dicots, a polyphyletic group. Basal angiosperms are a group of plants that are believed to have branched off before the separation into monocots and eudicots because they exhibit traits from both groups. They are categorized separately in many classification schemes, and correspond to a grouping known as the Magnoliidae, which includes magnolia trees, laurels, water lilies, and the pepper family.

Animals (Metazoa)

Two different groups within the Domain Eukaryota have produced complex multicellular organisms: The plants arose within the Archaeplastida, whereas the animals (and their close relatives, the fungi) arose within the Opisthokonta. However, plants and animals not only have different life styles, they also have different cellular histories as eukaryotes. The opisthokonts share the possession of a single posterior flagellum in flagellated cells, e.g., sperm cells.

The animal classification system characterizes animals based on their anatomy, features of embryological development, and genetic makeup. Scientists are faced with the task of classifying animals within a system of taxonomy that reflects their evolutionary history. Additionally, they must identify traits that are common to all animals as well as traits that can be used to distinguish among related groups of animals. However, animals vary in the complexity of their organization and exhibit a huge diversity of body forms, so the classification scheme is constantly changing as new information about species is learned.

Even though members of the animal kingdom are incredibly diverse, animals share common features that distinguish them from organisms in other kingdoms. All animals are eukaryotic, multicellular organisms, and almost all animals have specialized tissues. Most animals are motile, at least during certain life stages. Animals require a source of food to grow and develop. All animals are heterotrophic, ingesting living or dead organic matter. This form of obtaining energy distinguishes them from autotrophic organisms, such as most plants, which make their own nutrients through photosynthesis and from fungi that digest their food externally. Most animals reproduce sexually: The offspring pass through a series of developmental stages that establish a determined body plan, unlike plants, for example, in which the exact shape of the body is indeterminate. The body plan refers to the shape of an animal.

The kingdom of animals is informally divided into invertebrate animals, those without a backbone, and vertebrate animals, those with a backbone.

Invertebrates

Although in general we are most familiar with vertebrate animals, the vast majority of animal species, about 95%, are invertebrates. Invertebrates include a huge diversity of animals, millions of species in about 32 phyla, which we can just begin to touch on here. The current understanding of evolutionary relationships among animal phyla begins with the distinction between animals with true differentiated tissues, called Eumetazoa, and animal phyla that do not have true differentiated tissues, such as the sponges (Porifera) and the Placozoa. The Eumetazoa (those with differentiated tissues) are subdivided into radially symmetrical animals (Radiata) and bilaterally symmetrical animals (Bilateria). The Radiata include the cnidarians (e.g., jellyfish) and ctenophores. All other Eumetazoa are members of the Bilateria clade. Having a bilateral body plans allows cephalization, concentrating nervous tissues and sensory organs in the head of the organism. The bilaterally symmetrical animals are further divided into two groups depending whether the mouth or anus develops first during embryonic development. Protostomes (meaning mouth-first) consist of two distinct clades: the ecdysozoans (including nematodes [roundworms], tardigrades, and arthropods) and lophotrochozoans (including annelids, mollusks, and brachiopods). Arthropoda include insects, arachnids, and crustaceans, and dominate the animal kingdom with an estimated 85% of known species, with many still undiscovered or undescribed. Deuterostomes (meaning mouth-second) include the chordates (which include the vertebrates) and echinoderms. Echinodermata are named after their “prickly skin” (from the Greek “echinos” meaning “prickly” and “dermos” meaning “skin”). This phylum is a collection of about 7,000 described living species of exclusively marine, bottom-dwelling organisms, such as sea stars, sea cucumbers, sea urchins, and sand dollars. The chordates are named for the notochord, which is a flexible, rod-shaped structure that is found in the embryonic stage of all chordates and in the adult stage of some chordate species. In addition to the vertebrates, the phylum Chordata contains two clades of invertebrates: Urochordata (tunicates) and Cephalochordata (lancelets) (Fig 14.5).

Vertebrates

The vertebrates contain more than 60,000 described species, divided into major groupings of the lampreys, fishes, amphibians, reptiles, birds, and mammals. One of the first major steps in the evolution of vertebrates was the emergence of the quadrupeds in the form of the amphibians (Fig 14.5). A second step was the evolution of the amniotic egg, which, similar to the evolution of pollen and seeds in plants, freed terrestrial animals from their dependence on water for fertilization and embryonic development (Fig 14.5). Within the amniotes, modifications of keratinous epidermal structures have given rise to scales, claws, hair, and feathers. The scales of reptiles sealed their skins against water loss, while hair and feathers provided insulation to support the evolution of endothermy, as well as served other functions such as camouflage and mate attraction in the vertebrate lineages that led to birds and mammals.

Modern fishes include an estimated 31,000 species. Fishes were the earliest vertebrates, and jawless fishes were the earliest of these. Jawless fishes—the present day hagfishes and lampreys—have a distinct cranium and complex sense organs including eyes, distinguishing them from the invertebrate chordates. The jawed fishes evolved later and are extraordinarily diverse today. Gnathostomes or “jaw-mouths” are vertebrates that have jaws and include both cartilaginous and bony fishes. One of the most significant developments in early vertebrate evolution was the origin of the jaw, which is a hinged structure attached to the cranium that allows an animal to grasp and tear its food. The evolution of jaws allowed early gnathostomes to exploit food resources that were unavailable to jawless fishes. Jawed fishes are divided into the Chondrichthyes (the cartilaginous fishes, including sharks and rays) and Osteichthyes (the bony fishes, including the vast majority of present-day fish).

Amphibians are tetrapods including frogs and salamanders. The amniotes (reptiles, birds, and mammals) are distinguished from amphibians by their terrestrially adapted (shelled) egg and an embryo protected by amniotic membranes. The evolution of amniotic membranes meant that the embryos of amniotes could develop within an aquatic environment inside the egg. This led to less dependence on a water environment for development and allowed the amniotes to invade drier areas. This was a significant evolutionary change that distinguished them from amphibians, which were restricted to moist environments due to their shell-less eggs. In the past, the most common division of amniotes has been into classes Mammalia, Reptilia, and Aves. Birds are descended, however, from dinosaurs, so this classical scheme results in groups that are not true clades. Reptiles are tetrapods. Limbless reptiles (i.e., snakes) may have vestigial limbs and are classified as tetrapods because they are descended from four-limbed ancestors. Data now suggest that birds belong within the reptile clade, but they display a number of unique adaptations that set them apart. Unlike the reptiles, birds are endothermic, meaning they generate their own body heat through metabolic processes. The most distinctive characteristic of birds is their feathers, which are modified reptilian scales. Mammals are vertebrates that have hair and mammary glands used to provide nutrition for their young.

Fungi

The word fungus comes from the Latin word for mushrooms. Indeed, the familiar mushroom is a reproductive structure used by many types of fungi. However, there are also many fungus species that don’t produce mushrooms at all. Being eukaryotes, a typical fungal cell contains a true nucleus and many membrane-bound organelles. Fungi include an enormous variety of living organisms. While scientists have identified about 135,000 species of fungi, this is only a fraction of the more than 1.5 million species of fungus likely present on Earth. Edible mushrooms, yeasts, black mold, and the producer of the antibiotic penicillin, Penicillium notatum, are all members of the Fungi. Unicellular fungi are generally referred to as yeasts. Two common examples of unicellular fungi are baker’s yeast (Saccharomyces cerevisiae) and Candida species (the agents of thrush, a common fungal infection).

Fungi were once considered plant-like organisms; however, DNA comparisons have shown that fungi are more closely related to animals than plants. Fungi are not capable of photosynthesis: They use complex organic compounds as sources of energy and carbon. Some fungal organisms multiply only asexually, whereas others undergo both asexual reproduction and sexual reproduction. Most fungi produce a large number of spores that are disseminated by the wind.

Fungi often interact with other organisms, forming mutually beneficial or mutualistic associations. Fungi also cause serious infections in plants and animals. For example, Dutch elm disease is a particularly devastating fungal infection that destroys many native species of elm (Ulmus spp.). In humans, fungal infections are generally considered challenging to treat because, unlike bacteria, they do not respond to traditional antibiotic therapy since they are also eukaryotes. Fungi have many commercial applications. The food industry uses yeasts in baking, brewing, and wine making. Many industrial compounds are byproducts of fungal fermentation. Fungi are the source of many commercial enzymes and antibiotics.

Like plant cells, fungal cells are surrounded by a thick cell wall; however, the rigid layers contain the complex polysaccharides chitin and glucan and not cellulose that is used by plants. Chitin, also found in the exoskeleton of insects, gives structural strength to the cell walls of fungi. The cell wall protects the cell from desiccation and predators. Fungi have plasma membranes similar to other eukaryotes, except that the structure is stabilized by ergosterol, a steroid molecule that functions like the cholesterol found in animal cell membranes.

Most fungi are multicellular organisms. They display two distinct morphological stages: vegetative and reproductive. The vegetative stage is characterized by a tangle of slender thread-like structures called hyphae (singular, hypha), whereas the reproductive stage can be more conspicuous. A mass of hyphae is called a mycelium. It can grow on a surface, in soil or decaying material, in a liquid, or even in or on living tissue. Although individual hypha must be observed under a microscope, the mycelium of a fungus can be very large with some species truly being “the fungus humongous.” The giant Armillaria ostoyae (honey mushroom) is considered the largest organism on Earth, spreading across over 2,000 acres of underground soil in eastern Oregon; it is estimated to be at least 2,400 years old.

Like animals, fungi are heterotrophs: they consume complex organic compounds and do not photosynthesize. In addition, fungi do not fix nitrogen from the atmosphere. Like animals, they must obtain it from their diet. However, unlike most animals that ingest food and then digest it internally in specialized organs, fungi perform these steps in the reverse order. Fungi excrete enzymes into the environment to break down compounds outside of the cell, then they transport the broken down carbohydrates into the cell. Fungi are mostly saprobes, organisms that derive nutrients from decaying organic matter. They obtain their nutrients from dead or decomposing organic matter, mainly plant material. As with animal cells, the fungal storage polysaccharide is glycogen rather than starch, as found in plants.

Protists

Protists refer to eukaryotes that are not land plants, animals, or fungi. During the past two decades, the field of molecular genetics has demonstrated that some protists are more related to animals, plants, or fungi than they are to other protists. Therefore, not including animals, plants, and fungi make the kingdom Protista a paraphyletic group, meaning that it does not include all descendants of its common ancestor. For this reason, protist lineages originally classified into the kingdom Protista continue to be examined and debated. In the meantime, the term “protist” still is used informally to describe this tremendously diverse group of eukaryotes.

There are over 100,000 described living species of protists, and it is unclear how many undescribed species may exist. Since many protists live as commensals or parasites in other organisms and these relationships are often species-specific, there is a huge potential for protist diversity that matches the diversity of their hosts. Most protists are microscopic, unicellular organisms that are abundant in soil, freshwater, brackish, and marine environments. They are also common in the digestive tracts of animals and in the vascular tissues of plants. Others invade the cells of other protists, animals, and plants. Not all protists are microscopic. Some have huge, macroscopic cells, such as the plasmodia (giant amoebae) of myxomycete slime molds or the marine green alga Caulerpa, which can have single cells that can be several meters in size. Some protists are multicellular, such as the red, green, and brown seaweeds.

Viruses

Viruses are noncellular parasitic entities that cannot be classified within any domain. Nearly all forms of life, from prokaryotic bacteria and archaeans, to eukaryotes such as plants, animals, and fungi, have viruses that infect them. In fact, viruses exist in a sort of netherworld between a living organism and a nonliving entity. Living things grow, metabolize, and reproduce. In contrast, viruses are not cellular, do not have a metabolism or grow, and cannot divide by cell division. Viruses can copy, or replicate themselves; however, they are entirely dependent on resources derived from their host cells to produce progeny viruses—which are assembled in their mature form. No one knows exactly when or how viruses evolved or from what ancestral source because viruses have not left a fossil record. Some virologists contend that modern viruses are a mosaic of bits and pieces of nucleic acids picked up from various sources along their respective evolutionary paths. Most scholars agree that viruses don’t have a single common ancestor, nor is there a consensus hypothesis about virus origins.

Viruses are noncellular, meaning they are biological entities that do not have a cellular structure. They therefore lack most of the components of cells, such as organelles, ribosomes, and the plasma membrane. A virion consists of a nucleic acid core, an outer protein coating or capsid, and sometimes an outer envelope made of protein and phospholipid membranes derived from the host cell. Viruses may also contain additional proteins, such as enzymes, within the capsid or attached to the viral genome. The most obvious difference between members of different viral families is the variation in their morphology, which is quite diverse. An interesting feature of viral complexity is that the complexity of the host does not necessarily correlate with the complexity of the virion. In fact, some of the most complex virion structures are found in the bacteriophages—viruses that infect the simplest living organisms, bacteria.

Unlike nearly all living organisms that use DNA as their genetic material, viruses may use either DNA or RNA. The virus core contains the genome—the total genetic content of the virus. Viral genomes tend to be small, containing only those genes that encode proteins which the virus cannot get from the host cell. This genetic material may be single- or double-stranded. It may also be linear or circular. While most viruses contain a single nucleic acid, others have genomes divided into several segments. The RNA genome of the influenza virus is segmented, which contributes to its variability and continuous evolution, and explains why it is difficult to develop a vaccine against it.

In DNA viruses, the viral DNA directs the host cell’s replication proteins to synthesize new copies of the viral genome and to transcribe and translate that genome into viral proteins. Human diseases caused by DNA viruses include chickenpox, hepatitis B, and adenoviruses. Sexually transmitted DNA viruses include the herpes virus and the human papilloma virus (HPV), which has been associated with cervical cancer and genital warts.

RNA viruses contain only RNA as their genetic material. To replicate their genomes in the host cell, the RNA viruses must encode their own enzymes that can replicate RNA into RNA or, in the retroviruses, into DNA. These RNA polymerase enzymes are more likely to make copying errors than DNA polymerases, and therefore often make mistakes during transcription. For this reason, mutations in RNA viruses occur more frequently than in DNA viruses. This causes them to change and adapt more rapidly to their host. Human diseases caused by RNA viruses include influenza, hepatitis C, measles, and rabies. The HIV virus, which is sexually transmitted, is an RNA retrovirus.

The Challenge of Virus Classification

Because most viruses probably evolved from different ancestors, the systematic methods that scientists have used to classify prokaryotic and eukaryotic cells are not very useful. If viruses represent “remnants” of different organisms, then even genomic or protein analysis is not useful. Why?, Because viruses have no common genomic sequence that they all share. For example, the 16S rRNA sequence so useful for constructing prokaryote phylogenies is of no use for a creature with no ribosomes! Biologists have used several classification systems in the past. Viruses were initially grouped by shared morphology. Later, groups of viruses were classified by the type of nucleic acid they contained, DNA or RNA, and whether their nucleic acid was single- or double-stranded. However, these earlier classification methods grouped viruses differently, because they were based on different sets of characters of the virus. The most commonly used classification method today is called the Baltimore classification scheme, and is based on how messenger RNA (mRNA) is generated in each particular type of virus.

References

Adapted from:

Fowler, Roush, & Wise (2022). NSCC Academic Biology 1050. PressBooks. https://pressbooks.atlanticoer-relatlantique.ca/biology1050/

and

Clark, M.A., Douglas, M., and Choi, J. (2018). Biology 2e. OpenStax. Retrieved from https://openstax.org/books/biology-2e/pages/1-introduction