Emergence of eukaryotes

Further information: Eukaryote § Origin of eukaryotes

Chloroplasts in the cells of a moss

Modern taxonomy classifies life into three domains. The time of their origin is uncertain. The Bacteria domain probably first split off from the other forms of life (sometimes called Neomura), but this supposition is controversial. Soon after this, by 2 Ga,the Neomura split into the Archaea and the Eukarya. Eukaryotic cells (Eukarya) are larger and more complex than prokaryotic cells (Bacteria and Archaea), and the origin of that complexity is only now becoming known.^{[citation needed]}

Around this time, the first proto-mitochondrion was formed. A bacterial cell related to today's Rickettsia,which had evolved to metabolize oxygen, entered a larger prokaryotic cell, which lacked that capability. Perhaps the large cell attempted to digest the smaller one but failed (possibly due to the evolution of prey defenses). The smaller cell may have tried to parasitizethe larger one. In any case, the smaller cell survived inside the larger cell. Using oxygen, it metabolized the larger cell's waste products and derived more energy. Part of this excess energy was returned to the host. The smaller cell replicated inside the larger one. Soon, a stable symbiosis developed between the large cell and the smaller cells inside it. Over time, the host cell acquired some genes from the smaller cells, and the two kinds became dependent on each other: the larger cell could not survive without the energy produced by the smaller ones, and these, in turn, could not survive without the raw materials provided by the larger cell. The whole cell is now considered a single organism, and the smaller cells are classified as organelles called mitochondria.

A similar event occurred with photosynthetic cyanobacteria entering large heterotrophic cells and becoming chloroplasts.Probably as a result of these changes, a line of cells capable of photosynthesis split off from the other eukaryotes more than 1 billion years ago. There were probably several such inclusion events. Besides the well-established endosymbiotic theory of the cellular origin of mitochondria and chloroplasts, there are theories that cells led to peroxisomes, spirochetes led to ciliaand flagella, and that perhaps a DNA virus led to the cell nucleus,though none of them are widely accepted.

Archaeans, bacteria, and eukaryotes continued to diversify and to become more complex and better adapted to their environments. Each domain repeatedly split into multiple lineages, although little is known about the history of the archaea and bacteria. Around 1.1 Ga, the supercontinent Rodinia was assembling.The plant, animal, and fungi lines had split, though they still existed as solitary cells. Some of these lived in colonies, and gradually a division of labor began to take place; for instance, cells on the periphery might have started to assume different roles from those in the interior. Although the division between a colony with specialized cells and a multicellular organism is not always clear, around 1 billion years ago,the first multicellular plants emerged, probably green algae. Possibly by around 900 Ma true multicellularity had also evolved in animals.

At first, it probably resembled today's sponges, which have totipotent cells that allow a disrupted organism to reassemble itself. As the division of labor was completed in all lines of multicellular organisms, cells became more specialized and more dependent on each other; isolated cells would die.