The endosymbiont theory is the most widely accepted theory of eukaryotic evolution; however, its progression is still somewhat debated. According to the nucleus-first hypothesis, the ancestral prokaryote first evolved a membrane to enclose DNA and form the nucleus. Conversely, the mitochondria-first hypothesis suggests that the nucleus was formed after endosymbiosis of mitochondria.

Contrary to the endosymbiont theory, the eukaryote-first hypothesis proposes that the simpler prokaryotic and archaeal life forms evolved from the already existing complex eukaryotic cells.

Evidence for Endosymbiont Theory

Evidence for the endosymbiont theory comes from the many similarities that the eukaryotic organelles, like mitochondria and chloroplast, share with prokaryotic cells. Like the prokaryotic cells, mitochondria and chloroplasts contain circular, double-stranded genomes devoid of histones. These organelles also divide by the process of fission, similar to bacterial cell division, rather than by mitosis. Of the two membranes that surround them, the inner membranes resemble the bacterial plasma membrane in lipid and protein composition. Finally, the structure of genes, genetic code, and translational machinery (such as ribosomes) in these organelles are more similar to the prokaryotic machinery than eukaryotic.

LECA - Last Eukaryotic Common Ancestor

All eukaryotes are believed to have evolved from the Last Eukaryotic Common Ancestor or LECA about 1100 to 2300 million years ago. It is thought that LECA had already acquired endosymbionts like mitochondria and chloroplast by this stage. The new organelles made these ancestral cells more efficient and powerful, which allowed them to evolve novel characteristics such as multicellularity and cellular specialization. Their large cell size and internal compartmentalization also allowed their genomes to increase in size during the course of evolution. However, only a small portion of this genome encoded proteins; the major portion was non-coding DNA mostly involved in regulatory processes. The ability to turn genes on and off when required was key to cell specialization and responding to environmental changes. Phylogenetic and comparative genomic studies show five to six eukaryotic supergroups that evolved from LECA and later diverged into the plethora of life forms we see today.