23.1: Introduction

Organisms are classified into three domains: Archaea, Bacteria, and Eukarya. The first two lineages comprise all prokaryotic cells, and the third contains all eukaryotes. A very sparse fossil record prevents us from determining what the first members of each of these lineages looked like, so it is possible that all the events that led to the last common ancestor of extant eukaryotes will remain unknown. However, comparative biology of extant (living) organisms and the limited fossil record provide some insight into the evolution of Eukarya.

The earliest fossils found appear to be those of domain Bacteria, most likely cyanobacteria. They are about 3.5 to 3.8 billion years old and are recognizable because of their relatively complex structure and, for prokaryotes, relatively large cells. Most other prokaryotes have small cells, 1 or 2 µm in size, and would be difficult to pick out as fossils. Fossil stromatolites suggest that at least some prokaryotes lived in interactive communities, and evidence from the structure of living eukaryotic cells suggests that it was similar ancestral interactions that gave rise to the eukaryotes. Most living eukaryotes have cells measuring 10 µm or greater. Structures this size, which might be fossilized remains of early eukaryotes, appear in the geological record in deposits dating to about 2.1 billion years ago.

Characteristics of Eukaryotes

Data from these fossils, as well as from the study of living genomes, have led comparative biologists to conclude that 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. Cells with nuclei surrounded by a nuclear envelope with nuclear pores: 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. Chromosomes organized by histones: Each eukaryotic chromosome consists of a linear DNA molecule coiled around basic (alkaline) 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 (karyogamy) to create a diploid zygote nucleus.
8. Cell walls: It might be reasonable to conclude that the last common ancestor could make cell walls during some stage of its life cycle, simply because cell walls were present in their prokaryote precursors. However, not enough is known about eukaryotes’ cell walls and their development to know how much homology exists between those of prokaryotes and eukaryotes. If the last common ancestor could make cell walls, it is clear that this ability must have been lost in many groups.

In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon, called convergent evolution, is one reason why protist classification is so challenging. The emerging classification scheme groups the entire domain Eukarya into six “supergroups” that contain all of the protists as well as animals, plants, and fungi that evolved from a common ancestor (Figure 23.1.1). Each of the supergroups is believed to be monophyletic, meaning that all organisms within each supergroup are believed to have evolved from a single common ancestor, and thus all members are most closely related to each other than to organisms outside that group. There is still evidence lacking for the monophyly of some groups. Each supergroup can be viewed as representing one of many variants on eukaryotic cell structure. In each group, one or more of the defining characters of the eukaryotic cell—the nucleus, the cytoskeleton, and the endosymbiotic organelles—may have diverged from the "typical" pattern.

Figure \(\PageIndex{1}\): Eukaryotic supergroups. This diagram shows a proposed classification of the domain Eukarya. Currently, the domain Eukarya is divided into six supergroups. Within each supergroup are multiple kingdoms. Although each supergroup is believed to be monophyletic, the dotted lines suggest evolutionary relationships among the supergroups that continue to be debated.

Keep in mind that the classification scheme presented here represents just one of several hypotheses, and the true evolutionary relationships are still to be determined. The six supergroups may be modified or replaced by a more appropriate hierarchy as genetic, morphological, and ecological data accumulate. When learning about protists, it is helpful to focus less on the nomenclature and more on the commonalities and differences that illustrate how each group has exploited the possibilities of eukaryotic life.

Archaeplastida

Molecular evidence supports the hypothesis that all Archaeplastida are descendents of an endosymbiotic relationship between a heterotrophic protist and a cyanobacterium. The protist members of the group include the red algae and green algae. It was from a common ancestor of these protists that the land plants evolved, since their closest relatives are found in this group. The red and green algae include unicellular, multicellular, and colonial forms. A variety of algal life cycles exists, but the most complex is alternation of generations, in which both haploid and diploid stages are multicellular. A diploid sporophyte contains cells that undergo meiosis to produce haploid spores. The spores germinate and grow into a haploid gametophyte, which then makes gametes by mitosis. The gametes fuse to form a zygote that grows into a diploid sporophyte. Alternation of generations is seen in some species of Archaeplastid algae, as well as some species of Stramenopiles. In some species, the gametophyte and sporophyte look quite different, while in others they are nearly indistinguishable. We will cover the non-protist Archaeplastids (land plants) in a later lab.

Figure \(\PageIndex{2}\): Volvox. Volvox aureus is a green alga in the supergroup Archaeplastida. This species exists as a colony, consisting of cells immersed in a gel-like matrix and intertwined with each other via hair-like cytoplasmic extensions. (credit: Dr. Ralf Wagner)

Amoebozoa

Like the Archaeplastida, the Amoebozoa include species with single cells, species with large multinucleated cells, and species that have multicellular phases. Amoebozoan cells characteristically exhibit pseudopodia that extend like tubes or flat lobes. These pseudopods project outward from anywhere on the cell surface and can anchor to a substrate. The protist then transports its cytoplasm into the pseudopod, thereby moving the entire cell. This type of motion is similar to the cytoplasmic streaming used to move organelles in the Archaeplastida, and is also used by other protists as a means of locomotion or as a method to distribute nutrients and oxygen. The Amoebozoa include both free-living and parasitic species.

Figure \(\PageIndex{3}\): Cellular Slime Mold. The image shows several stages in the life cycle of Dictyostelium discoideum, including aggregated cells, mobile slugs and their transformation into fruiting bodies with a cluster of spores supported by a stalk. (credit: By Usman Bashir (Own work) [CC BY-SA 4.0 ([creativecommons.org])], via Wikimedia Commons)

Opisthokonta

The Opisthokonts are named for the single posterior flagellum seen in flagellated cells of the group. The flagella of other protists are anterior and their movement pulls the cells along, while the opisthokonts are pushed. Protist members of the opisthokonts include the animal-like choanoflagellates, which are believed to resemble the common ancestor of sponges and perhaps, all animals. Choanoflagellates include unicellular and colonial forms (Figure 23.1.4), and number about 244 described species. In these organisms, the single, apical flagellum is surrounded by a contractile collar composed of microvilli. The collar is used to filter and collect bacteria for ingestion by the protist. A similar feeding mechanism is seen in the collar cells of sponges, which suggests a possible connection between choanoflagellates and animals.

The Mesomycetozoa form a small group of parasites, primarily of fish, and at least one form that can parasitize humans. Their life cycles are poorly understood. These organisms are of special interest, because they appear to be so closely related to animals. In the past, they were grouped with fungi and other protists based on their morphology. We will cover the non-protist Opisthokonts (animals and fungi) in later labs.

Figure \(\PageIndex{4}\): A Colonial Choanoflagellate. (credit: By Dhzanette ([en.Wikipedia.org]) [Public domain], via Wikimedia Commons)

The previous supergroups are all the products of primary endosymbiontic events and their organelles—nucleus, mitochondria, and chloroplasts—are what would be considered "typical," i.e., matching the diagrams you would find in an introductory biology book. The next three supergroups all contain at least some photosynthetic members whose chloroplasts were derived by secondary endosymbiosis. They also show some interesting variations in nuclear structure, and modification of mitochondria or chloroplasts.

Rhizaria

The Rhizaria supergroup includes many of the amoebas with thin threadlike, needle-like or root-like pseudopodia (Figure 23.1.5), rather than the broader lobed pseudopodia of the Amoebozoa. Many rhizarians make elaborate and beautiful tests—armor-like coverings for the body of the cell—composed of calcium carbonate, silicon, or strontium salts. Rhizarians have important roles in both carbon and nitrogen cycles. When rhizarians die, and their tests sink into deep water, the carbonates are out of reach of most decomposers, locking carbon dioxide away from the atmosphere. In general, this process by which carbon is transported deep into the ocean is described as the biological carbon pump, because carbon is “pumped” to the ocean depths where it is inaccessible to the atmosphere as carbon dioxide. The biological carbon pump is a crucial component of the carbon cycle that maintains lower atmospheric carbon dioxide levels. Foraminiferans are unusual in that they are the only eukaryotes known to participate in the nitrogen cycle by denitrification, an activity usually served only by prokaryotes.

Figure \(\PageIndex{5}\): Rhizaria. Ammonia tepida, a Rhizaria species viewed here using phase contrast light microscopy, exhibits many threadlike pseudopodia. It also has a chambered calcium carbonate shell or test. (credit: modification of work by Scott Fay, UC Berkeley; scale-bar data from Matt Russell)

Foraminiferans

Foraminiferans, or forams, are unicellular heterotrophic protists, ranging from approximately 20 micrometers to several centimeters in length, and occasionally resembling tiny snails (Figure 23.1.6). As a group, the forams exhibit porous shells, called tests that are built from various organic materials and typically hardened with calcium carbonate. The tests may house photosynthetic algae, which the forams can harvest for nutrition. Foram pseudopodia extend through the pores and allow the forams to move, feed, and gather additional building materials. Typically, forams are associated with sand or other particles in marine or freshwater habitats. Foraminiferans are also useful as indicators of pollution and changes in global weather patterns.

Figure \(\PageIndex{6}\): Foraminiferan Tests. These shells from foraminifera sank to the sea floor. (credit: Deep East 2001, NOAA/OER)

Radiolarians

A second subtype of Rhizaria, the radiolarians, exhibit intricate exteriors of glassy silica with radial or bilateral symmetry (Figure 23.1.7). Needle-like pseudopods supported by microtubules radiate outward from the cell bodies of these protists and function to catch food particles. The shells of dead radiolarians sink to the ocean floor, where they may accumulate in 100 meter-thick depths. Preserved, sedimented radiolarians are very common in the fossil record.

Figure \(\PageIndex{7}\): Radiolarian shell. This fossilized radiolarian shell was imaged using a scanning electron microscope. (credit: modification of work by Hannes Grobe, Alfred Wegener Institute; scale-bar data from Matt Russell)

Chromalveolata

Current evidence suggests that species classified as chromalveolates are derived from a common ancestor that engulfed a photosynthetic red algal cell, which itself had already evolved chloroplasts from an endosymbiotic relationship with a photosynthetic prokaryote. Therefore, the ancestor of chromalveolates is believed to have resulted from a secondary endosymbiotic event. However, some chromalveolates appear to have lost red alga-derived plastid organelles or lack plastid genes altogether. Therefore, this supergroup should be considered a hypothesis-based working group that is subject to change. Chromalveolates include very important photosynthetic organisms, such as diatoms, brown algae, and significant disease agents in animals and plants. The chromalveolates can be subdivided into alveolates and stramenopiles.

Figure \(\PageIndex{8}\): Dinoflagellate bioluminescence. Bioluminescence is emitted from dinoflagellates in a breaking wave, as seen from the New Jersey coast. (credit: “catalano82”/Flickr)

Figure \(\PageIndex{9}\): Paramecium. Paramecium has a primitive mouth (called an oral groove) to ingest food, and an anal pore to eliminate waste. Contractile vacuoles allow the organism to excrete excess water. Cilia enable the organism to move. (credit “paramecium micrograph”: modification of work by NIH; scale-bar data from Matt Russell)

Figure \(\PageIndex{10}\): Diatoms. Assorted diatoms, visualized here using light microscopy, live among annual sea ice in McMurdo Sound, Antarctica. Diatoms range in size from 2 to 200 µm. (credit: Prof. Gordon T. Taylor, Stony Brook University, NSF, NOAA)

Excavata

Many of the protist species classified into the supergroup Excavata are asymmetrical, single-celled organisms with a feeding groove “excavated” from one side. This supergroup includes heterotrophic predators, photosynthetic species, and parasites. Its subgroups are the diplomonads, parabasalids, and euglenozoans. The group includes a variety of modified mitochondria, as well as chloroplasts derived from green algae by secondary endosymbiosis. Many of the euglenozoans are free-living, but most diplomonads and parabasalids are symbionts or parasites.

Figure \(\PageIndex{11}\): Giardia. The mammalian intestinal parasite Giardia lamblia, visualized here using scanning electron microscopy, is a waterborne protist that causes severe diarrhea when ingested. (credit: modification of work by Janice Carr, CDC; scale-bar data from Matt Russell)