All complex life, from single-celled algae to giant sequoias and blue whales, belongs to the domain Eukaryota. Eukaryotic cells are defined by a nucleus that houses genetic material and other specialized compartments called organelles, distinguishing them from simpler prokaryotes like bacteria. To understand how this diversity of life is related, scientists use phylogeny, the study of evolutionary history. These relationships are often depicted in a branching diagram called a phylogenetic tree, which maps the connections from the earliest eukaryotic ancestors to the vast array of species present today.
The Origins of Eukaryotic Complexity
The journey of eukaryotes began more than 1.5 billion years ago with endosymbiosis. This theory proposes that the organelles of eukaryotic cells were once independent prokaryotes. The process began when a larger host cell engulfed smaller prokaryotes, forming a permanent, mutually beneficial relationship.
The origin of mitochondria resulted from an ancestral eukaryote engulfing an aerobic bacterium capable of using oxygen to generate energy. Over time, this engulfed bacterium became the mitochondrion, the “powerhouse” of the cell. Evidence for this includes mitochondria having their own circular DNA, similar to bacteria, and replicating independently within the cell.
A similar endosymbiotic event occurred in the lineage leading to plants and algae when a eukaryotic cell that already contained mitochondria engulfed a photosynthetic cyanobacterium. This engulfed cell evolved into the chloroplast, the organelle responsible for photosynthesis. This secondary event gave rise to the capacity for photosynthesis in the eukaryotic domain, providing the foundation for all plant and algal life.
Methods for Mapping Eukaryotic Relationships
Scientists use several methods to reconstruct the eukaryotic evolutionary tree. Early studies relied on morphology, comparing physical characteristics like cellular anatomy and fossil records. These comparisons provided the first maps of eukaryotic relationships but were sometimes misleading due to convergent evolution, where similar traits evolve independently.
Molecular biology provided a more direct record of evolutionary change by comparing sequences of DNA, RNA, and proteins. The degree of similarity between sequences from different organisms indicates how closely related they are. Fewer differences suggest a more recent common ancestor, while a greater number of differences implies a more distant relationship.
The analysis of ribosomal RNA (rRNA) has been a useful molecular tool, as its gene is present in all living organisms and changes slowly, making it ideal for comparing deeply divergent groups. More recently, phylogenomics analyzes vast datasets comprising hundreds or even thousands of genes. This method provides a more robust and detailed picture of the eukaryotic tree, helping to resolve relationships that were once unclear.
The Major Eukaryotic Supergroups
The modern understanding of eukaryotic diversity organizes life into several large branches known as supergroups. These groupings are based on extensive molecular data and represent the primary divisions that occurred after the initial emergence of eukaryotes. Each supergroup contains a vast collection of organisms, from single-celled microbes to familiar multicellular life forms.
The Archaeplastida supergroup includes red algae, green algae, and all land plants. The defining characteristic is that their chloroplasts derive from a single, primary endosymbiotic event involving a cyanobacterium. This makes them the direct descendants of the first photosynthetic eukaryotes, with examples from microscopic algae to redwood trees.
Another massive supergroup is SAR, an acronym for Stramenopila, Alveolata, and Rhizaria. This group is united by DNA sequence data, as its members are morphologically different. Stramenopiles include diatoms and brown algae; Alveolates include ciliates and dinoflagellates; and Rhizaria are amoeboid microbes with intricate skeletons, like foraminiferans.
The supergroup Excavata is composed of single-celled organisms, many defined by a distinctive “excavated” feeding groove. This group includes free-living predators, photosynthetic species, and parasites like Giardia lamblia, which causes intestinal illness in humans.
Amoebozoa is the supergroup containing many organisms called amoebas, as well as slime molds. These organisms use lobe-shaped pseudopods for movement and feeding. While many are unicellular, some slime molds aggregate into multicellular structures under certain conditions.
Finally, the supergroup Opisthokonta includes animals, fungi, and their closest single-celled relatives, the choanoflagellates. The name “Opisthokonta” refers to a single, posterior flagellum in their motile cells, such as animal sperm. The close evolutionary relationship between animals and fungi, revealed by molecular data, was a surprising discovery.
Evolution of Classification Systems
The classification of eukaryotic life has moved from systems based on observable traits to one grounded in evolutionary history. For much of the 20th century, the five-kingdom system was dominant, dividing life into Monera (prokaryotes), Protista, Fungi, Plantae, and Animalia. This system grouped organisms based on broad characteristics like nutrition and cellular organization.
The development of molecular phylogenetics exposed limitations of this model. Genetic analyses demonstrated that the five kingdoms did not represent the true evolutionary lineages. The most significant issue was with Kingdom Protista, which served as a catch-all category for any eukaryote that was not a plant, animal, or fungus.
Molecular evidence revealed that members of the former Kingdom Protista are scattered across the eukaryotic tree. For instance, algae are in both the Archaeplastida and SAR supergroups, while amoeboid organisms are in Amoebozoa and Rhizaria. This showed that “Protista” was not a monophyletic group (one descended from a single common ancestor) and was invalid, leading to the supergroup classification system.