Contrary to what researchers long thought, our distant ancestors were not microbes that thrived in boiling hot springs or deep within giant ice sheets. A new evolutionary analysis of eukaryotes—the group of organisms that includes everything from mushrooms to humans—suggests that they descended from a group of microbes common in oceans and soils.
In the 1970s, microbiologist Carl Woese of the University of Illinois, Urbana-Champaign, proposed a new way to classify life. Instead of comparing physical characteristics as previous scientists had done, he compared short gene sequences. Where researchers had once separated all organisms into five major groups, including bacteria, plants, and animals, Woese's method split living things among three domains: bacteria, eukarya, and archaea. The scheme combined all eukaryotes, which are organisms whose DNA is enclosed in a nucleus, into one large group, and split the prokaryotes, which are organisms whose DNA is not contained in a nucleus, into the bacteria and archaea. The bacteria includes the familiar microbes that cause disease and help make yogurt, whereas the archaea includes microbes that live in extreme environments, like boiling hot water emerging from volcanic vents at the bottom of the ocean. Over the past 30 years, a large body of evidence has confirmed Woese's results.
However, scientists still didn't know how eukaryotes originated. To find out, Steven Kelly, a computational biologist at the University of Oxford in the United Kingdom, and colleagues analyzed more than 3500 groups of genes with similar functions to create an evolutionary tree for the archaea. The researchers then tried to join their new phylogenetic tree with the most accurate trees for either bacteria or eukaryotes. They assumed that the bacteria and eukaryotes were connected to the archaea by a single organism and tried to find which group of archaea was most closely related to the eukaryotes. They then created hundreds of different trees by changing which species of archaea evolved into what would become the ancestor to all modern-day eukaryotes. Finally, the researchers calculated the likelihood that each tree was correct based on their gene family DNA sequences.
Kelly and colleagues found that eukaryotes are most closely related to a recently discovered family of archaea known as Thaumarchaea. Unlike many archaea, which thrive in boiling hot sulfuric acid or within Arctic ice sheets, the Thaumarchaea prefer the much more moderate environment of temperate ocean waters and soils. "[Thaumarchaea] can make up about 30% of all the organisms in some temperate oceans," says Kelly, whose team will report its findings online tomorrow in the Proceedings of the Royal Society B. "They're very abundant in soils as well, and they fill an important ecological niche" by producing nitrates that enhance plant growth.
"It had always bothered me that eukaryotes [were thought to] come out of this really hot origin," says Joel Dacks, a biologist at the University of Alberta in Canada. The Thaumarchaea prefer similar temperatures as modern eukaryotes and share some genetic similarities, such as the way they replicate their DNA, he says, bolstering the case that the first eukaryote descended from a member of Thaumarchaea.
Previous hypotheses had suggested that eukaryotes evolved alongside archaea, and both groups had descended from the same ancestor. In recent years, genetic data has raised doubts about the accuracy of these hypotheses, and Kelly says that his data pretty much put the final nail in the coffin. His results, he says, clearly show that archaea evolved first, and then eukaryotes evolved from a particular family of archaea.
"This study is excellent," Dacks concludes. "It's a nice piece of science, and it's a nice example of how to think and communicate clearly."