Rooting eukaryotes in the Arctic Ocean

While the general consensus has centered around the evolution of eukaryotes within the TACK superphylum of Archaea (Thaum-, Aigar-, Cren-, and Kor-archaeota), considerable controversy yet remains with (a) the rooting of the eukaryote common ancestor, and (b) ‘missing’ links in several eukaryote genes which have no known origin within the TACK superphylum. Two recent manuscripts attempt to answer these questions with some very intriguing finds.

Deep sea vents in Loki’s Castle, ~4000 ft below sea level, a grand playground for Archaea, and possibly the eukaryotic common ancestors. Image courtesy: ethlife.ethz.ch/archive_articles/121101_black_smoker_per

An 18th century depiction of the Norse God, Loki, often described as “a staggeringly complex, confusing, and ambivalent figure who has been the catalyst of countless unresolved scholarly controversies”. Image courtesy: Wikipedia

  • The two-domain tree of life is linked to a new root for the Archaea – Raymann et al. (2015) PNAS

Raymann et al. (2015) report phylogenomic reconstructions using markers shared between Archaea and eukaryotes (as against previous studies that utilize only universal consensus trees). The authors test three possible scenarios for the placement of eukaryotes – (1) eukaryotes being sister to Euryarchaeota, (2) eukaryotes being sister to TACK superphylum, and (3) both scenarios 1 and 2, and eukaryotes are sister to all of Archaea. Re-analyses thus strongly suggests support for scenario (3), and the emergence of eukaryotes from a branch of Archaea, called the Euryarchaeota.

Our results strongly suggest that an emergence of eukaryotes from within the Archaea is tightly linked to a root within Euryarchaeota. Therefore, if we are to embrace an archaeal origin for eukaryotes, we must also reconsider our view of the emergence and evolution of the third domain of life.

  • Complex archaea that bridge the gap between prokaryotes and eukaryotes – Spang et al. (2015) Nature

Echoing the rhetoric from the above paper, how indeed did eukaryotes evolve from within Archaea? Eukaryotic genomes are chimeric, with bacterial and archaeal origin genes. But while most bacterial origin genes have been traced (to mitochondrial progenitor alphaproteobacteria), and few archaeal origin genes have been primarily traced to TACK superphyla, several missing links exist (as indicated by Raymann et al. (2015)). Spang et al. (2015) in this monumental discovery report phylogenetic support for the “bridge” between TACK archaea, and eukaryotes – Lokiarcheota, a newly discovered species of Archaea surveyed from the depths of the Arctic Ocean. Metagenomic analyses reveal the monophyly of eukaryotes with Lokiarcheota, whose genome encodes several eukaryotic genes.

The proposed naming of the Eukarya-affiliated candidate phylum Lokiarchaeota and the Lokiarchaeum lineage is made in reference to the sampling location, Loki’s Castle, which in turn was named after the Norse mythology’s shape-shifting deity Loki. Loki has been described as “a staggeringly complex, confusing, and ambivalent figure who has been the catalyst of countless unresolved scholarly controversies”, in analogy to the ongoing debates on the origin of eukaryotes.

References:

Kasie Raymann, Céline Brochier-Armanet, and Simonetta Gribaldo “The two-domain tree of life is linked to a new root for the Archaea.”  PNAS (2015). DOI: http://dx.doi.org/10.1073/pnas.1420858112

Spang, Anja, et al. “Complex archaea that bridge the gap between prokaryotes and eukaryotes.” Nature (2015). DOI: http://dx.doi.org/10.1038/nature14447

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About Arun Sethuraman

I am a computational biologist, and I build statistical models and tools for population genetics. I am particularly interested in studying the dynamics of structured populations, genetic admixture, and ancestral demography.
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