A new Tree of Life; Archaea and Eukaryotes related? (Evolution)

by David Turell , Tuesday, June 05, 2018, 15:29 (2151 days ago) @ David Turell

A new branch of Archaea has some genes that are Euykaryote genes:

https://www.the-scientist.com/?articles.view/articleNo/54649/title/Archaea-Family-Tree-...

“[Archaeal taxonomy is] kind of like the Wild West,” says Brett Baker, a microbial ecologist at the University of Texas at Austin. “There’s going to be a huge debate about how we define a phylum.”

The Asgard superphylum, described by Ettema, Baker, and their colleagues in 2017, is also generating some disagreement due to its implications for the evolution of eukaryotes. The research started out innocuously enough, as the scientists assembled the genomes of an archaeal group found in sediments near an Arctic deep-sea vent known as Loki’s Castle.5 But they saw something strange. “We started finding all these eukaryotic genes,” Ettema recalls, including genes that seemed to encode eukaryote-like cytoskeletal proteins, small GTPases, and the ESCRT machinery involved in membrane-based processes such as autophagy and lysosome-based protein degradation.6 These so-called “eukaryotic signature proteins” typically don’t have homologs in either bacteria or archaea, says Ettema. “I realized either this is something really interesting, or this is some freaky artifact.”

He and his colleagues tested the samples for evidence of true eukaryotes, such as their 18S rRNA, and came up empty-handed. Convinced that the microbes they identified were indeed archaea, the researchers reported their results in 2015, dubbing the new phylum Lokiarchaeota for the vent site.7 Since then, Ettema’s and Baker’s teams have found three sister phyla to Lokiarchaeota, all containing genes formerly thought to be specific to eukaryotes: the Thorarchaeota, found in the dark, tannic acid–stained White Oak River estuary of North Carolina;8 the Odinarchaeota, found in hot springs such as those in Yellowstone National Park;9 and the Heimdallarchaeota, discovered in marine sediments.9 The researchers grouped these together as the Asgard superphylum.

Based on their interrogations of the asgardians, Ettema, Baker, and colleagues concluded that these archaea fit neatly into the late Lynn Margulis’s longstanding hypothesis of endosymbiosis—the idea that eukaryotes arose when one microbe engulfed another. The Asgard archaea would seem to be descendants of the original host that swallowed a bacterium, and at that time already possessed some of the genes scientists would come to associate with eukaryotes. This contrasts with the older idea that archaea and eukaryotes sprang from a common ancestor and evolved as two distinct, parallel lineages. The Lokiarchaeota provided the turning point, says Ettema: “Suddenly we come up with this phylum that seems to turn everything around.” He notes that Lokiarchaeota’s name references not only the discovery site but also the Norse trickster god for that reason.

Eme, who works in Ettema’s lab, says she’s now analyzing about 60 new Asgard genomes, looking for more eukaryote-like features and trying to piece together how the group evolved. “Now that we have more representatives of each of the lineages . . . we are starting to be able to make more-confident claims,” she says. “There’s so much to understand from these archaea.”

Comment: If Archaea came first bacteria and Eukaryotes are their descendents