Bacteria and Archaea are the two major divisions of the tree of life. Eukaryotes evolved from a group of prokaryotic archaea that captured and incorporated at least two different bacteria through endosymbiosis. Environmental genomic studies have revealed a much higher diversity of prokaryotes than was previously known.

Question 1

Before DNA sequencing was developed, biologists usually grouped all prokaryotes together, emphasizing the differences between eukaryotes and prokaryotes. But the characteristics that differentiated these two “groups” (such as the presence of a nucleus, or the various organelles) are all derived features of eukaryotes. When gene sequences were compared across all of life (especially the ribosomal RNA genes, which are easily compared across all living organisms), it became clear that the diversity among “prokaryotes” was far greater than the diversity among eukaryotes. Indeed, it soon became apparent that the ribosomal RNA genes of prokaryotic archaea were actually more similar to the ribosomal genes of eukaryotes than they were to the ribosomal RNA genes of bacteria, and Archaea was proposed as a domain separate from Bacteria. As biologists studied Archaea in more detail, they discovered that many other features were also distinct from Bacteria.

Question 2

Question 3

The genomes of eukaryotes contain mostly genes that are more closely related to prokaryotic archaea than to bacteria. This leads biologists to conclude that an ancestral prokaryotic archaean lineage first acquired the features that are characteristic of eukaryotes (such as the nucleus). These early eukaryotes then acquired an endosymbiotic proteobacterium, which was eventually incorporated as the eukaryote mitochondrium. Later, one group of eukaryotes acquired another endosymbiont, this time an early cyanobacterium, which became the chloroplast of photosynthetic eukaryotes.