Eukaryotes are cells commonly identified by the presence of a nucleus. Eukaryota is one of the three domains of life (bacteria and archea are the others and collectively referred to as prokaryotes) and encompasses single-celled organisms as well as all multicellular life. The evolution of eukaryotes is rather unique because it is substantially non-Darwinian; where Darwinian evolution largely concerns itself with beneficial genes arising by mutation and then spreading through differential reproductive success, the story of eukaryotes is one of significant horizontal gene flow (the exchange of genes across species) and of distinct organisms fusing into entirely new organisms.

Eukaryotes contain a variety of structures that distinguish them from prokaryotes (archea and bacteria), most notably the nucleus and a host of organelles (endoplasmic reticulum, Golgi bodies, peroxisomes, mitochondria, chloroplasts, etc.). They also possess flagella of unique structure (containing microtubules) and cytoskeletal structures made of microtubules and microfilaments (neither of which is found in prokaryotes). Eukaryotes also often organize their DNA around histones (proteins that act like spools) and package it into chromosomes. Some eukaryotes also participate in some form of sexual reproduction though many retain the ability to reproduce asexually.

Timing of the emergence of earliest eukaryotes is greatly debated. The first evidence of eukaryotes puts their origin at about 2.3-1.6 billion years ago. This range is derived primarily from phylogenetic analyses. Multicellular algae fossils are dated at 1.2 billion years, thus providing an absolute lower bound while fossils of single-celled organisms resembling algae are dated to around 2.2 billion years old, though scientists debate whether these represent eukaryotes or are merely similar in appearance.

Most calculations place the oldest eukaryotes close to the first global glaciation approximately 2.3 billion years ago. It is believed that a rise in the number in photo-synthetic prokaryotes led to an increase in oxygen, which resulted in global cooling. This increase in oxygen is believed to have decimated populations of anaerobic pro-karyotes. Some scientists believe that eukaryotes existed in low abundance before the rise in oxygen while others believe they originated shortly after. Scientists do agree however that the rise in oxygen is likely responsible for their increase in abundance and rise to multicellularity.

It is important to note that much of the theories regarding the origins of eukaryotes are speculative and it is unlikely that any one hypothesis will ever be championed above all others. However, as we sequence more genomes (particularly those of proposed early eukaryotes, and complete genome sequences of organisms from all domains of life) and develop more sophisticated phylo-genetic techniques, it will be possible to narrow the likely possibilities.

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