The Princeton Guide to Evolution

II.12

Origin and Diversification of Eukaryotes

Laura A. Katz and Laura Wegener Parfrey

OUTLINE

1. Origin of eukaryotes

2. Timing of the origin and diversification of eukaryotes

3. A brief history of eukaryotic classification

4. Major clades of eukaryotes

5. Distribution of photosynthesis in eukaryotes

6. Extant symbioses

7. Genome diversity in microbial eukaryotes

8. Origins of multicellularity

Eukaryotes are marked by tremendous diversity in terms of size, shape, ecology, and genome structure. Eukaryotes are defined by two evolutionary innovations: the nucleus and cytoskeleton. Although named for the presence of a nucleus (eu = true, karyon = kernel or seed), it is the cytoskeleton and related proteins that allowed for the dramatic variation in morphology (i.e., shape and size) among eukaryotes. As with Archaea and Bacteria, the other two domains of life, eukaryotes are predominantly single-celled microbes, with plants, animals, and fungi representing just three of approximately 75 major lineages. This chapter discusses the origin of eukaryotes and current views of the relationships among eukaryotic lineages, and then highlights the diversity of eukaryotes by exploring the distribution of several characters (e.g., photosynthesis and multicellularity) across these lineages.

GLOSSARY

Algae (Sing., Alga). A descriptive term for any photosynthetic (i.e., plastid-containing) eukaryote. Algae are broadly distributed across the eukaryotic tree of life and are not a monophyletic group. The term can refer to taxa that have primary, secondary, or tertiary plastids.

Amoebae. A descriptive term for microbial eukaryotes that move using cytoplasmic projections called pseudopodia. Amoeboid organisms are found in many different lineages of eukaryotes.

Cytoskeleton. The cellular scaffolding that is made out of proteins and gives eukaryotes their shape, enables cellular movement, and participates in many subcellular processes.

Endosymbiosis. The intimate associate of two organisms where one (endosymbiont) lives within the other (host). Ancient endosymbiotic events led to the acquisition of mitochondria and plastids, both of which have played a large role in shaping the evolutionary history of eukaryotes.

Lateral Gene Transfer. Transfer of genetic material between distantly related organisms, by nonsexual means, in contrast to vertical inheritance of genes from parent to offspring. Lateral gene transfer obscures the structure of the tree of life.

Nucleus. A double-membrane-bound organelle that contains the genome, is the site of transcription, and is present in all eukaryotic cells.

Plastid. An organelle derived from the endosymbiosis of an algal cell (either cyanobacterium or eukaryotic alga). Plastids are generally involved in photosynthesis and include the chloroplasts of plants.

Protist. A descriptive term for eukaryotes that are not plants, animals, or fungi, used most commonly for microbial taxa. Protists do not constitute a monophyletic clade, and early classifications that lumped protists together in groups such as Protista or Protozoa are invalid.

Slime Molds. A diverse collection of organisms found in at least five of the major clades of eukaryotes originally thought to be fungi, because they form a multicellular fruiting body and release spores at one stage in their life cycle.

1. ORIGIN OF EUKARYOTES

The events that led to the origin of eukaryotes remain one of the outstanding questions in biology. Hypotheses put forth to explain the origin of eukaryotes must account for the presence of three features of eukaryotic cells: nucleus, cytoskeleton, and mitochondria. The nucleus and cytoskeleton are the defining features of eukaryotes, and both are absent in Bacteria and Archaea. These features must, therefore, have been present in the ancestral eukaryote, though their origins remain unclear. Research over the past two decades has demonstrated that mitochondria were also present in the last common ancestor of all extant eukaryotes, although they subsequently evolved into reduced mitochondria-related organelles in numerous lineages. In contrast to the nucleus and cytoskeleton, the mechanisms for the origin of mitochondria has been robustly established: they were acquired through endosymbiosis of an alphaproteobacterium. We discuss the origin of these defining features of eukaryotes in relation to hypotheses on the origin of the eukaryotic domain. Such hypotheses can generally be divided into those that invoke endosymbiosis and those that assume an autogenous mechanism (evolution within a single lineage).

The origin of the eukaryotic cytoskeleton, which gives eukaryotes their distinct morphologies and motilities, remains a mystery. The renowned biologist Lynn Margulis argued that the eukaryotic cytoskeleton resulted from endosymbiosis between an archaeon and a spirochete (a bacterium); however, no eukaryotic cytoskeletal proteins appear to have evolved specifically from within the spirochetes. Although homologues of some cytoskeletal proteins have been found in bacteria (e.g., FtsZ and MreB are bacterial homologues of tubulin and actin, respectively), evidence is lacking that the eukaryotic proteins derive from any specific bacterial lineage. Moreover, the bulk of eukaryotic cytoskeletal proteins lack clear homologues in either of the other domains; hence, it is unclear how the many proteins underlying the cytoskeleton arose.

Similarly, few data or convincing models exist to explain the origin of the eukaryotic nucleus and the associated endoplasmic reticulum. Many hypotheses argue that the nucleus resulted from an endosymbiotic event between a bacterium and an archaeon, two different bacteria, or even between an archaeon and a virus; however, few proteins within the nucleus show convincing affinities with any specific lineage of bacteria or archaea. Other theories posit an autogenous origin of the nucleus, driven by a selection pressure such as separation of transcription and translation or protection from viruses. The nuclear envelope provides spatial separation of transcription and translation in eukaryotes, whereas these processes occur in close proximity in Bacteria and Archaea. This has led to the suggestion that one advantage of the nuclear envelope is to allow for processing of pre-mRNAs (e.g., removal of introns) prior to translation. Other hypotheses posit that the nucleus arose as an autogenous product of the endosymbiotic event that gave rise to mitochondria. Additional data are needed to support or reject these hypotheses.

One of the few certainties in the origin and diversification of eukaryotes is that mitochondria, found in many but not all eukaryotes, are derived from an endosymbiotic alphaproteobacterium. Evidence for this symbiotic origin includes the membrane structure of mitochondria, its mode of division, and the presence of a bacterial-derived genome whose genes have close affinity to homologous genes in the Alphaproteobacteria. Moreover, the preponderance of evidence indicates that the acquisition of mitochondria occurred prior to the evolution of the last common ancestor of all extant eukaryotes. This evidence includes the broad phylogenetic distribution of mitochondria on the eukaryotic tree of life. While some eukaryotic lineages without mitochondria do exist, such as Trichomonas, Giardia, some ciliates, and some fungi, their nested relationships amongmitochondrial-containing taxa demonstrates that their ancestors had mitochondria. In fact, eukaryotes originally thought to completely lack mitochondria turn out to have double-membrane-bound organelles derived from mitochondria. These remnant mitochondria are alternatively termed hydrogenosomes if they are anaerobic and hydrogen-producing, or mitosomes if they are highly reduced.

2. TIMING OF THE ORIGIN AND DIVERSIFICATION OF EUKARYOTES

Eukaryotes likely arose in the Paleoproterozoic, 2.1–1.7 billion years ago. This estimate emerges from the first appearance of putative eukaryotes in the fossil record as well as from molecular clock analyses (see chapter II.3 for a discussion of molecular clock dating). The earliest fossils of eukaryotes are found around 1800 million years ago (Ma) and cannot be assigned to any extant clade. These fossils are identified as eukaryotes because they have complex structures that require a cytoskeleton to build, or inferred behaviors (e.g., budding) found only in eukaryotes. For example, fossils have been found from 1500 Ma with a cell wall composed of hexagons (akin to the patterning of a soccer ball) and others have been found covered with cylindrical processes that extend symmetrically from the cell. During the early evolution of eukaryotes, earth was very different from today: oceans were predominantly anoxic and sulfidic, and complex multicellular life was absent.

Fossils that can be assigned to modern clades of eukaryotes begin to appear around 1200 Ma with the appearance of the red algal fossil Bangiomorpha. Molecular clock analyses suggest that all the major clades of eukaryotes appeared prior to 1000 Ma and were present for hundreds of millions of years before leaving fossil evidence. Beginning 800 Ma, the diversity and abundance of eukaryotic fossils increases markedly: there are testate (shelled) amoebae and green algal fossils as well as biomarkers (fossilized lipids that indicate the presence of particular groups of organisms) that suggest the presence of ciliates and other taxa. The radiation of many eukaryotic lineages around 800 Ma coincides with a shift in the chemistry of the oceans toward conditions beginning to resemble modern oceans in that they became more fully oxygenated and were no longer sulfidic.

3. A BRIEF HISTORY OF EUKARYOTIC CLASSIFICATION

The relationships among eukaryotes have been subject to much debate and revision, as have the definitions of the groups themselves. Early classification schemes such as those of Carl Linneaus divided the living world into plants and animals, so that all photosynthetic eukaryotes (both multicellular and microbial) were considered plants (i.e., “algae”) and motile microbes were considered animals (i.e., “protozoa,” including ciliates, flagellates, and amoebae). This worldview is problematic from a modern perspective because it does not entail naming of natural (i.e., monophyletic; see chapter II.8) groups. Moreover, many microbial taxa fall into both categories at the same time, such as the photosynthetic amoeba Paulinella (see section 5 below).

Following Charles Darwin’s publication of On the Origin of Species in 1859, representations of biodiversity were transformed to capture the concepts of ancestors and descendants. For example, Ernst Haeckel’s 1866 depiction of the “Tree of Life” divided living things into Plantae, Animalia, and Protista. The Protista included a grab bag of problematic organisms such as amoebae, flagellates, ciliates, fungi, some animals (e.g., sponges), and bacteria. The concept of these basic divisions persisted into the 1970s with the development of the five-kingdom system. Four of these five kingdoms of life are eukaryotic: plants, animals, fungi, and protists; however, from an evolutionary perspective, these divisions are inappropriate, because “protists” are nonmonophyletic—animals, plants, and fungi all evolve from within microbial lineages. Thus, labels such as protist and alga remain useful as descriptive terms, but have no phylogenetic meaning.

In recent decades, molecular data have redrawn the fundamental division of living organisms into three domains (bacteria, archaea, and eukaryotes), all of which are predominately microbial. This classification was first created based on the evolutionary history of a single gene that is part of the ribosome of all living beings: the small subunit ribosomal RNA. Additional genes and a few differences in cell structure also support the three-domain concept of life; however, extensive lateral gene transfer among many lineages complicates the concept of the tree of life as evolution has occurred through a combination of vertical and lateral descent (chapter II.11). For example, the acquisitions of mitochondria and plastids represent dramatic examples of lateral transfer in which an entire genome from one lineage is captured by another through endosymbiosis.

In the past decades, we have gained a much better understanding of relationships among eukaryotes from analyses of molecular data combined with insights from ultrastructure—details of subcellular structures that are revealed by electron microscopy. Beginning in the 1960s it was found that protists comprise 70+ lineages that can be distinguished on the basis of ultrastructural features. We now understand that animals, plants, and fungi emerge out of these microbial lineages, indicating that the distinction between macroscopic and microscopic eukaryotes is a false one, driven by an excessive focus on the world we can physically see. Molecular data have confirmed the monophyly of the majority of the lineages defined by ultrastructure. In recent years, most of these lineages have been characterized with molecular data from multiple genes (which yield more robust results than single gene analyses) and have been grouped into four major clades: Opisthokonta, Amoebozoa, Excavata, and SAR (Stramenopiles + Alveolates + Rhizaria). For example, more than 30 of the 70+ lineages defined by ultrastructural identities have been shown to fall within the Rhizaria. Thus, the phylogenetic relationships among eukaryotes are stabilizing, although the placement of some photosynthetic lineages and other “orphan lineages” is still subject to debate. We discuss each of these major clades below.

4. MAJOR CLADES OF EUKARYOTES

The Opisthokonta unite the animals and fungi along with their microbial relatives. The affinity of animals with choanoflagellates was first noted more than a century ago; specialized sponge cells termed choanocytes have similar structure as choanoflagellates (see chapter II.15). The Opisthokonta are the best supported of the major clades in molecular studies, and also share the morphological trait of a single posterior flagellum (in clades with flagella) and the molecular synapomorphy of an insertion into the EF-1α gene (see chapters II.1 and II.8 for definitions of phylogenetic terms). Other members of the group include the Ichthyosporea (parasites of fish) and an enigmatic slime mold called Fonticula. Thus, multicellularity evolved many times within the Opisthokonta (see section 8 below for a discussion of multicellularity in eukaryotes, and chapter II.14 for fungi).

The Amoebozoa include many of the organisms typically called “amoebae,” including the star of high school biology Amoeba proteus, two clades of slime molds, and Entamoeba histolytica, the causative agent of amoebic dysentery; however, this clade does not contain all amoebae, since amoeboid lineages can be found in virtually every major clade of eukaryotes. Amoebozoa emerged out of molecular phylogenetic analyses and are generally recovered in multigene molecular analyses, but there is no defining synapomorphy for Amoebozoa. The largest clade within the Amoebozoa, the Tubulinea, does have a morphological synapomorphy: cylindrical pseudopodia in which the cytoplasm streams in just one direction (monoaxial streaming). Examples of Tubulinea include the lobose testate (shelled) amoebae whose fossilized remains have been so useful in reconstructing paleoclimate and our old friend Amoeba.

The Excavata were originally defined on the basis of a morphological and ultrastructural character, an “excavated” ventral feeding groove. The clade is only sometimes recovered, and then only in molecular analyses with many genes and dense taxonomic sampling. The most familiar Excavata are the causative agents of parasitic diseases. These include Giardia, a major cause of diarrhea worldwide that exacerbates malnutrition in children in the developing world. Other parasitic excavates include trypanosomes that cause sleeping sickness and Trichomonas vaginalis, which causes the sexually transmitted disease trichomoniasis. Members of Excavata are heterotrophic with the exception of one lineage of euglenids (a close relative of the trypanosomes) that acquired photosynthetic ability by engulfing a green alga endosymbiont hundreds of millions of years ago (see section 5). Many taxa, and all the parasites, within the Excavata are anaerobic and have highly reduced mitochondria, either hydrogenosomes or mitosomes. Some of these parasites also have rapid rates of evolution that artificially pulled them to the base of early ribosomal DNA trees (see chapter II.2 for a discussion of long-branch attraction artifacts). These two observations led to the now-disproven hypothesis that members of the Excavata represented early diverging eukaryotes that had branched off the eukaryotic lineage prior to the acquisition of mitochondria.

The final major clade of eukaryotes that is moderately well supported, SAR, is the amalgamation of the three other monophyletic clades, the stramenopiles, alveolates, and rhizarians. The stramenopiles contain diatoms (algae with beautiful silica shells), kelps, and the causative agent of the Irish potato famine (Phytophthora). The alveolates include the morphologically diverse ciliates, the dinoflagellates critical to the survival of coral reefs, and the apicomplexa, which include the malaria parasite. Both the stramenopiles and alveolates are defined by ultrastructural synapomorphies. The stramenopiles have specific hairs on one of their flagella and the alveolates have sacs (alveoli) underlying their cell membrane that lend rigidity. In contrast, Rhizaria is a large, heterogeneous collection of amoebae, flagellates, and parasitic lineages that lacks diagnostic ultrastructural features. The amoeboid members of Rhizaria tend to have filose (fine) or reticulating networks of pseudopodia, a morphological feature that generally (but not always) distinguishes Rhizaria from members of the Amoebozoa. The SAR clade also contains the largest number of named species among the microbial eukaryotes, as it contains the diatoms, ciliates, and foraminifera, each encompassing thousands of described species.

The phylogenetic position of lineages that are wholly or predominantly photosynthetic is much less resolved. This instability is likely driven by gene transfer from the algal symbionts to the host nucleus, complicating phylogenetic reconstruction. The most popular hypothesis is that all the primary photosynthetic lineages (green algae, red algae, and glaucophytes) form a monophyletic clade, and that a single endosymbiotic event in the ancestor of this clade gave rise to all plastids (see section 5 for more information on plastids).

5. DISTRIBUTION OF PHOTOSYNTHESIS IN EUKARYOTES

The shift from historical classification systems that lumped together all photosynthetic organisms toward a system emphasizing monophyletic groups has led to the realization that photosynthesis is patchily distributed across eukaryotes (figure 1). Much of the energy that powers ecosystems—terrestrial, marine, and freshwater—is driven by photosynthetic eukaryotes making up the diverse clades of algae (including land plants, a lineage of green algae). Photosynthesis in eukaryotes was likely acquired through endosymbiosis of a single cyanobacterium more than a billion years ago, much like the endosymbiosis of an alphaproteobacterium that led to mitochondria. Like mitochondria, plastids have a small, circular genome with roughly 100 genes. As the cyanobacterium was reduced to a plastid, many of the genes in the cyanobacterial genome were lost, and others were transferred to the host nucleus. Today the chloroplasts of plants contain about 110–120 genes, and the plant nucleus contains many times that number: generally around 10 percent of a plant’s nuclear genome is derived from cyanobacteria.

Figure 1. Cartoon tree of eukaryotes that highlights the lineages discussed in the text. The dashed line connecting red algae, green algae, and glaucophytes reflects the remaining uncertainty about this relationship. Symbols indicate the trait is found in at least one member of the clade. Multicellularity: + = multicellular lineages; +* = multiple origins of multicellularity; A = aggregative multicellularity such as slime molds. Photosynthesis: 1° = primarily photosynthetic lineages; 2° = secondarily photosynthetic. E = Extant symbioses with algae.

The prevailing hypothesis is that the initial acquisition of plastids occurred only once in the ancestor of all primary photosynthetic lineages. Evidence in support of this hypothesis includes the similarity among all plastids in the transport machinery that moves macromolecules from the host to and from the plastid, and the similarity of the plastid genes themselves according to phylogenetic analyses; however, the possibility that plastids were acquired multiple times cannot be ruled out at this time, mainly because the three lineages thought to be direct descendants of that single acquisition, the primary photosynthetic lineages (red algae, green algae, and glaucophytes), are not monophyletic in many phylogenetic analyses. Moreover, cyanobacteria appear to have gone through substantial extinction and radiation events since the time of the endosymbiosis, making inferences about the ancestry of plastids more difficult.

After the initial establishment of photosynthesis in eukaryotes, plastids spread through the eukaryotic tree of life by secondary, tertiary, and even quaternary endosymbiosis. Secondary endosymbiosis is the engulfment of a unicellular alga by a nonphotosynthetic eukaryote. In all known cases, secondary endosymbiosis involves red or green algae (glaucophytes are not known to have become secondary plastids). Rather than being fully digested, the alga is retained, reduced, and over many generations, fully integrated into the host cell as a secondary plastid. In most lineages, the reduction process has resulted in the loss of all the components of the symbiotic algal cell except for the plastid; however, two distantly related lineages, the cryptomonads and chlorarachniophytes, still have a remnant nucleus from the red and green algal symbiont, respectively. A now-defunct hypothesis placed the six or more lineages (including dinoflagellates and photosynthetic stramenopiles) with secondary red algal plastids into a clade called chromalveolates; however, it is now clear that secondary endosymbiosis involving red algae has occurred multiple times across the eukaryotic tree of life.

There are also photosynthetic endosymbioses that are established but have not (yet) proceeded to the point where the retained alga can be considered a plastid. One such case is a second example of a primary endosymbiosis of a cyanobacterium by the amoeba Paulinella (within Rhizaria). Several photosynthetic lineages of Paulinella have been isolated from around the world and it is estimated that this endosymbiosis began about 65 Ma.

Other lineages of eukaryotes take advantage of photosynthesis despite their lack of fully integrated plastids. Instead they rely on plastids that are retained from food organisms (termed kleptoplastids) or on extant symbioses with algal lineages. The process of kleptoplasty (retaining stolen plastids) gives us green, photosynthetic animals like the sea slug Elysia. Similarly, Foraminifera and Radiolaria (large amoebae that fall within the Rhizaria) include many members that reside in the upper layers of the oceans and farm algae, generally dinoflagellates. During the day these amoebae expose the symbiotic algae to sunlight by extending them in their extensive pseudopodial network to photosynthesize, and at night the algae are drawn back into the amoeba cell body and sugars are harvested.

6. EXTANT SYMBIOSES

Extant eukaryotes are involved in many important symbioses, where they can serve as either hosts or symbionts, or both. For example, corals are an association between animals (host) and photosynthetic dinoflagellates (symbionts) in which the dinoflagellates provide the cnidarian host with sugars and amino acids and the coral provides nutrients and protection. When this symbiosis goes awry, the corals can suffer, as is the case in coral bleaching, which arises when dinoflagellates leave in response to high temperatures or stress. The “green animals” and “farming amoebae” discussed above harbor algal symbionts within their tissues, presumably to take advantage of the energy produced by photosynthesis.

Symbioses involving heterotrophic eukaryotes are also rampant; for example, ciliates and parabasalid flagellates aid in the digestion of cellulose in ruminants (e.g., cows) and the hindguts of termites. Microbial eukaryotes can also play host to symbiotic bacteria, archaea, or other eukaryotes, and some of these symbioses play a role in human health. Some amoebae within the Amoebozoa are able to serve as Trojan horses, harboring pathogenic bacteria that can eventually emerge and cause disease. In 1976, for example, numerous people were sickened at an American Legion convention in Philadelphia by bacteria (later assigned to the genus Legionella) that were harbored inside amoebae. Since then, considerable effort has been spent documenting the numerous bacteria that can live within microbial eukaryotes. Associations between eukaryotes and bacterial endosymbionts can also alter the pathogenicity of human parasites such as Trichomonas and Entamoeba. For example, in the presence of pathogenic Escherichia and Salmonella bacteria, Entamoeba becomes much more invasive and causes more tissue damage.

7. GENOME DIVERSITY IN MICROBIAL EUKARYOTES

Textbooks generally depict genomes as stable entities that are passed from generation to generation with minimal change. While this is generally true, there is a surprising amount of variation across eukaryotes in the genome content both within individual organisms during their life cycle and among individuals belonging to the same species. The most common forms of genome variation are ploidy-level variation (shifts in copy number of the whole genome beyond haploid and diploid) and differential amplification of portions of the genome. The extensive variation in genome content within individuals during their life cycle suggests that eukaryotes have the ability to distinguish between the genome that will be inherited in the next generation (i.e., germ line genome) and the somatic genome that accumulates variation during the life of a cell.

In many lineages, the germ line and somatic genomes are segregated into separate nuclei (in the same or different cells). Animals are the most familiar case of segregated genomes, with germ line cells sequestered early in development. In some animals, including copepods, nematodes, and hagfish, the somatic genome is extensively modified from the zygote, as chromosomes are fragmented and a portion of the genome is eliminated. Ciliates are also characterized by the presence of two types of nuclei that contain genetically different genomes, the micronucleus (germ line) and the macronucleus (somatic), though both these genomes exist within a single cell. The micronuclear genome behaves like a typical eukaryotic genome in that it goes through meiosis and mitosis and has a few long chromosomes; in contrast, the genome of the macronucleus is fragmented, sometimes extensively, yielding hundreds to thousands of tiny somatic chromosomes. Foraminifera are the third lineage with genetically distinct somatic and germ line genomes, although this feature is present only in a subset of genera. Here one of the nuclei in the multinucleate life cycle stage expands and is transcriptionally active while the remaining generative nuclei are quiescent until meiosis.

8. ORIGINS OF MULTICELLULARITY

Contrary to the popular belief that multicellularity is rare, involving only plants, animals, and fungi, there have been many origins of multicellularity among eukaryotes (figure 1). For example, many lineages of algae have become multicellular. Several of these multicellular algae are familiar, including giant kelps and the red algae used in making sushi. There are also multiple origins of multicellularity among the green algae, among whose descendants are the land plants. Further, there have been several origins of multicellularity in terrestrial environments where organisms have evolved to produce multicellular fruiting bodies that likely aid in dispersal. Such organisms constitute the numerous lineages of slime molds, which include the dictyostelids and acrasids as well as isolated genera scattered across the eukaryotic tree (figure 1). Comparative analyses that include these lesser-known origins of multicellularity may be helpful in clarifying the selective pressures and developmental mechanisms underlying the origin of multicellularity.

Synthesis

Eukaryotes, cells defined by the presence of both a nucleus and a cytoskeleton, have inhabited the earth for nearly 2 billion years. During this time, eukaryotes have evolved into a tremendous diversity of forms found in all major ecosystems. The bulk of eukaryotic diversity is microbial, though we are most familiar with the macroscopic lineages: plants, animals, and fungi. While the combination of powerful microscopes and molecular data have begun to transform our understanding of the origin and diversification of eukaryotes, there is still much to be discovered about this incredible branch on the tree of life.