Origin of Eukaryotes: The Rise of Complex Cells on Earth

The origin of eukaryotes, cells with a nucleus and internal compartments, was one of the most important steps in the history of life. Complex cells probably arose somewhere between about 2 and 1.6 billion years ago, when a host cell related to archaea joined forces with a bacterium that became the mitochondrion. Every animal, plant and fungus, including humans, descends from that partnership.

Two kinds of cell

All living things are built from one of two basic kinds of cell. Prokaryotes, the bacteria and archaea, are small and relatively simple, with their DNA lying free inside the cell. Eukaryotes are typically much larger and contain a nucleus wrapped in a membrane, an internal skeleton, and organelles such as mitochondria, the structures that generate most of the cell’s energy.

For more than a billion years after life began, Earth was home only to prokaryotes. Microbial mats and stromatolites flourished in shallow seas, and cyanobacteria released the oxygen that built up during the Great Oxidation Event around 2.4 to 2.1 billion years ago. Eukaryotes appeared after this change, and most scientists think the rise of oxygen made their energy-demanding lifestyle possible.

Endosymbiosis: cells inside cells

The key to the origin of eukaryotes is endosymbiosis, a relationship in which one organism lives inside another. In 1905 the Russian botanist Konstantin Mereschkowski suggested that chloroplasts, the green organelles of plants, were descended from cyanobacteria that had taken up residence inside other cells.

The idea was largely ignored until 1967, when the American biologist Lynn Margulis, then publishing as Lynn Sagan, argued in “On the origin of mitosing cells” that mitochondria and chloroplasts both had a bacterial origin. Her paper was rejected by many journals before publication, and the theory was controversial for years.

Genetic evidence later proved the core of her argument. Mitochondria and chloroplasts have their own small circular genomes, divide like bacteria and have bacterial-type ribosomes. DNA comparisons show that mitochondria descend from alphaproteobacteria, and chloroplasts from cyanobacteria.

Over time, most of the original bacterial genes were lost or transferred to the host cell’s nucleus. Human mitochondria, for example, keep only 37 genes of their own.

The host cell

A remaining question was the identity of the cell that took in the ancestor of the mitochondrion. Since the 1970s it has been known that archaea, a group of microbes recognised by Carl Woese and colleagues, share some features with eukaryotes.

In 2015 researchers studying DNA from sediments near a hydrothermal vent field in the Arctic Ocean, known as Loki’s Castle, described a new group of archaea, the Lokiarchaeota. Related lineages, collectively called Asgard archaea, carry genes once thought to be unique to eukaryotes. In 2020 a Japanese team succeeded in growing one of these microbes in the laboratory after more than a decade of work.

Many researchers now favour a scenario in which an Asgard-related archaeon and an alphaproteobacterium formed a close partnership, perhaps exchanging hydrogen or other chemicals, which eventually became permanent. The biochemist Nick Lane and the biologist William Martin have argued that the energy supplied by mitochondria was what allowed eukaryotic cells to grow larger and more complex than bacteria.

Fossil evidence

Identifying the earliest eukaryotes in rocks is difficult, because single cells rarely fossilise and many bacteria can look similar under a microscope.

Early candidates

Coiled, ribbon-like fossils called Grypania spiralis, found in the Negaunee Iron Formation of Michigan and dated to roughly 1.87 billion years old, may be early eukaryotic algae, although some researchers think they could be large bacterial colonies. Older claimed evidence, such as the Francevillian biota of Gabon, about 2.1 billion years old, remains debated.

Chemical fossils were once thought to push the record back further. Traces of steranes, molecules derived from sterols that are characteristic of eukaryotic membranes, were reported in 1999 from 2.7-billion-year-old rocks in Australia. Later work showed that these molecules were contamination from younger sources.

Widely accepted fossils

The oldest widely accepted eukaryotic microfossils are about 1.6 to 1.7 billion years old, from the Changcheng Group of northern China and similar rocks in northern Australia. Some of these cells have complex walls or surface ornaments that only eukaryotes are known to produce.

Palaeontologists look for several features when deciding whether a microfossil is eukaryotic: a large size, complex wall structures, spines or other ornaments, and signs of a flexible cell that could change shape. No single feature is decisive, so the identification of early fossils often rests on a combination of clues.

In 2001 Emmanuelle Javaux, Andrew Knoll and Malcolm Walter described diverse eukaryotic microfossils from the Roper Group of northern Australia, about 1.5 billion years old, including the spiny form Tappania. By about 1.05 billion years ago, the red alga Bangiomorpha pubescens from Arctic Canada shows multicellularity and is often cited as the oldest known evidence of sexual reproduction.

Myths and facts

Myth: eukaryotes evolved gradually from bacteria by becoming more complex. Genetic evidence points instead to a merger: the eukaryotic cell combines an archaeal host with a bacterial partner, and its genome contains genes from both. Many details, including the order in which the nucleus and mitochondria appeared, are still debated.

Myth: the first complex cells were plants or animals. The earliest eukaryotes were single-celled microbes, broadly similar to modern protists. Plants arose much later, after a eukaryote engulfed a cyanobacterium that became the chloroplast; that second partnership gave rise to green algae, red algae and their relatives, and eventually land plants.

Myth: the date is precisely known. Molecular clock estimates for the last common ancestor of all living eukaryotes range from roughly 1.9 to 1 billion years ago, depending on the method and the fossils used for calibration. The fossil record and the molecular evidence have not yet been fully reconciled.

The “Boring Billion” and beyond

For hundreds of millions of years after their appearance, eukaryotes remained a modest part of ecosystems dominated by bacteria. This long interval, roughly 1.8 to 0.8 billion years ago, is sometimes called the “Boring Billion” because climate and ocean chemistry changed relatively little.

The picture changed in the Neoproterozoic Era. Eukaryotic algae became ecologically important around 800 to 650 million years ago, and the first animals appeared before the Cambrian explosion about 539 million years ago, when most major animal groups appear in the fossil record.

Timeline

• c. 2.4–2.1 billion years ago: The Great Oxidation Event brings free oxygen into the atmosphere.
• c. 2.0–1.8 billion years ago: Possible early eukaryotes, including Grypania, appear in the fossil record (disputed).
• c. 1.65 billion years ago: Widely accepted eukaryotic microfossils occur in northern China.
• c. 1.5 billion years ago: Diverse eukaryotic microfossils, including Tappania, live in the seas of northern Australia.
• c. 1.05 billion years ago: The red alga Bangiomorpha shows multicellularity and sexual reproduction.
• 1905: Konstantin Mereschkowski proposes that chloroplasts come from symbiotic cyanobacteria.
• 1967: Lynn Margulis (as Lynn Sagan) publishes her endosymbiotic theory of mitochondria and chloroplasts.
• 2015: Lokiarchaeota, the first of the Asgard archaea, are described from Arctic seabed sediments.

Why it matters

The origin of eukaryotes made complex life possible. Without the energy supplied by mitochondria, cells may never have grown large or diverse enough to form seaweeds, forests, fungi and animals. The story also shows that some of evolution’s biggest steps came not from gradual change alone but from cooperation between very different organisms that became one.