Supergroups

All the challenges to the first genetic tree of life “left us with a mess,” Keeling says. It became clear that the history of all eukaryotes cannot be reconstructed in any sensible tree based on one gene. “We ripped it all apart and put it back together. And it came together very differently.”

Instead of a crown of multicellular groups rising over relicts on long branches, the organisms “coalesced in a small number of very large groups,” he says.

The new arrangement, summarized in 2012 by Sina Adl of the University of Saskatchewan and colleagues in the Journal of Eukaryotic Micro­biology, makes a fabulous mix of convergence and divergence. Animals are close relatives of fungi. Both are opisthokonts, along with some one-celled cousins. A Phytophthora potato pathogen, once famous as the “fungus” that caused famine in Ireland in the 1840s, is not a fungus at all. It belongs in the same supergroup as the giant kelp. Red and green seaweeds join plants in a distinct group called the archaeplastids.

These are big, deep-history groups, but don’t call them kingdoms. “Alastair is allergic to kingdoms,” Roger says of Simpson. The two collaborated on a 2002 paper enumerating supergroups instead.

Simpson wanted a term no one would treat as a formal rank. “ ‘Kingdom’ has such gravitas,” he says, not admiringly. Biologists assign kingdom rank based largely on subjective impressions, so he sees little information conveyed just by knowing something is a kingdom instead of some other rank in a hierarchy. To avoid the whole nonsense, he uses supergroup in a lighthearted nod to bands such as the Traveling Wilburys, which united (briefly) Bob Dylan, George Harrison and three other independently famous musicians.

Diatoms (top) with glasslike casings belong in the stramenopile supergroup. They come in diverse shapes, including the fanlike diatom (bottom) that lives on red algae, which are archaeplastids.

From Top: FRANK FOX/WIKIMEDIA COMMONS (CC BY-SA 3.0 DE); © WENN Ltd/Alamy

Like Dylan and the others, each biological supergroup has its own illustrious story. The proposed one that Simpson found most surprising united all modern eukaryote groups that have algae with chlorophyll c. That’s a huge crowd with no other obvious trait in common. Although chloro­phyll c organisms seem so different at first sight, Cavalier-Smith suggested that they all descended from one eukaryote that swallowed another, which became its photosynthesizing organelle. “It seemed a very bold hypothesis,” Simpson says.

Sequential swallowings are a big part of eukaryote history. Engulfers were themselves engulfed and in turn engulfed yet again. “Like matryoshka dolls,” Keeling says.

Some genetic evidence now links three big groups to a single ancestral engulfment of chlorophyll c, Simpson says. Stramenopiles, with giant kelp and potato pathogens, now join alveolates and rhizaria (even though they have no chlorophyll c) as what’s often abbreviated as SAR. Other chlorophyll c carriers are still under study, so the bold hypothesis might someday turn out to be right. “The really cool thing is, we still don’t know the answer,” Simpson says.

This and other eukaryotic mysteries may resolve more easily as geneticists refine a technique for deciphering DNA from one individual cell. Nature Methods called it “method of the year” for 2013.

The technique’s possibilities intrigue researchers because single-celled species can be difficult or impossible to grow in the lab. Roger lovingly describes radiolarians, some of which build skeletons of strontium sulfate while others manage to eat multicelled animals. “Just beautiful organisms,” he says, but “they’re a real pain actually to work on.” Single-cell DNA sequencing has helped in the study of bacteria, and papers here and there report results for eukaryotes. The technique revealed an interplay of chemistry between a termite-gut dweller and its own live-in spirochete bacteria in work published May 15 in the Proceedings of the National Academy of Sciences.

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