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The Three Domain Hypothesis: RIP

The Three Domain Hypothesis died about twenty years ago but most people didn't notice.

The original idea was promoted by Carl Woese and his colleagues in the early 1980s. It was based on the discovery of archaebacteria as a distinct clade that was different from other bacteria (eubacteria). It also became clear that some eukaryotic genes (e.g. ribosomal RNA) were more closely related to archaebacterial genes and the original data indicated that eukaryotes formed another distinct group separate from either the archaebacteria or eubacteria. This gave rise to the Three Domain Hypothesis where each of the groups, bacteria (Eubacteria), archaebacteria (Archaea), and eukaryotes (Eucarya, Eukaryota), formed a separate clade that contained multiple kingdoms. These clades were called Domains.

The two most important features of the Three Domain Hypothesis are: (1) there are three distinct domains, and (2) the eukaryotic domain is more closely related to archaebacteria than to the other domain of bacteria. Both of these claims are wrong. We now know that some of the nuclear genes in eukaryotes arose from within the Archaea domain so there aren't three domains. We now know that most of the nuclear genes in eukaryotes are more closely related to genes from eubacteria than to genes from archaebactreial species so the tree of life shown on the left misrepresents the origin of eukaryotes.

Early skeptics of the Three Domain Hypothesis

The PR machine orchestrated by Carl Woese and Norman Pace was spectacularly successful so that by the early 1990s almost everyone was convinced that the Three Domain Hypothesis was correct and it became part of standard textbook dogma. However, there were a few skeptics. One of the most prominent was Jim Lake who argued that eukaryotes arose from within Archaea. He pointed out that eukaryotic genes appeared to be more similar to the genes from Eocytes than other branches of the Archaea tree suggesting that eukaryotes share a more recent common ancestor with Eocytes than other groups [Jim Lake and the Eocyte tree].

The skeptics were subjected to harsh criticism from the PR machine so that the reputations of scientists like Jim Lake suffered greatly. However, more and more evidence for this tree has emerged over the past thirty years so that almost all researchers in this field now agree that the tree of life is a Two-Domain tree with some eukaryotic genes sharing a common ancestor with the Asgard group of archaea from within the the Archaea Domain. Here's the latest paper on this subject—it's what prompted me to write this post.
Williams, T.A., Cox, C.J., Foster, P.G., Szöllősi, G.J., and Embley, T.M. (2020) Phylogenomics provides robust support for a two-domains tree of life. Nature ecology & evolution, 4:138-147. [doi: 10.1038/s41559-019-1040-x]

Hypotheses about the origin of eukaryotic cells are classically framed within the context of a universal ‘tree of life’ based on conserved core genes. Vigorous ongoing debate about eukaryote origins is based on assertions that the topology of the tree of life depends on the taxa included and the choice and quality of genomic data analysed. Here we have reanalysed the evidence underpinning those claims and apply more data to the question by using supertree and coalescent methods to interrogate >3,000 gene families in archaea and eukaryotes. We find that eukaryotes consistently originate from within the archaea in a two-domains tree when due consideration is given to the fit between model and data. Our analyses support a close relationship between eukaryotes and Asgard archaea and identify the Heimdallarchaeota as the current best candidate for the closest archaeal relatives of the eukaryotic nuclear lineage.
The figure below is from a review of the paper by Gribaldo and Brochier-Armanet (2020). It illustrates the difference between a three-domain tree and a two-domain tree.

I should draw your attention to the quality of the discussion in the Williams et al. paper. It contains a lengthy introduction concerning the controversy over three-domain and two-domain trees and the data supporting each tree. The experiments in the paper are designed to distinguish between the two possibilities and the results and conclusion section contain critical analyses of the results and how they compare to other data. This is the way scientific papers should be written.1

Experienced readers will immediately recognize part of the problem from looking at the figure above. It's the issue of long branch attraction—a phenomenon that can artifactually cluster two long branches such as the bacterial and eukaryotic branches. This will produce a three-domain tree that does not faithfully represent the true tree of life. The authors of the paper try to correct for this (presumed) artifact by using sophisticated phylogenetics software and Bayesian relative rate tests. I'm more than a little skeptical about whether the quality of the underlying data can support such manipulations but, nevertheless, it makes a lot of sense that some eukaryotic genes arose from within the Archaea.2

The ring of life

One of the distinguishing features of eukaryotic cells is that they contain mitochondria that are clearly descendants of an endosymbiotic event where an archaeal cell engulfed a primitive alphaproteobacterium. Over time, a good proportion of the alphaproteobacterial genes migrated to the nucleus so that a typical eukaryotic genome now contains a majority of genes that are proteobacterial in origin (see the figure below from McInerney and O'Connell, 2017).
What this means is that it is extremely misleading to represent the origin of eukaryotes as simply the descendants of a single archaeal species. Both of the genomes involved in the original fusion contributed to the modern eukaryotic genome.

Endosymbiosis is not new but it took some time for scientists to realize that the contribution of alphaproteobactrial genes was very significant and that the original Three Domain Hypothesis was misleading. Eventually this idea came to be known as the Ring of Life (e.g. McInerney et al, 2014 [see figure on the right]; McInerney et al., 2015; Lake, 2015)

Proponents of the Three Domain Hypothesis dismissed the evidence for a ring of life by claiming that some genes were more important than others in constructing ancient phylogenies. It became a major talking point to assume that ribosomal RNA genes and genes for proteins involved in translation and transcription were the only ones that count in determining the origin of eukaryotes (informational genes). Since these genes tend to be more similar to archaea than to eubacteria, it lent support to the Three Domain Hypothesis. Indeed, as late as 2009 Norman Pace was still arguing that the Three Domain Hypothesis was valid because the small subunit RNA genes (SSU) were the only reliable phylogenetic marker (Pace, 2009).

ThemeThe Three Domain HypothesisHowever, by that time there was increasing evidence that the genes arose from within Archaea casting doubt on the existence of a separate Eucarya domain and furthermore, there were well-informed researchers who pointed out that the great majority of eukaryotic genes (~80%) that are more closely related to Eubacteria than to Archaea are genes involved in fundamental aspects of metabolism. It seems rather silly to trace the origin of eukaryotes by only looking at a biased subset of eukaryotic genes and ignoring the majority that give a different result (see "The Tree of One percent," Dagan and Martin, 2006) (see "The real 'domains' of life," Walsh and Doolittle, 2005).

What's interesting about this controversy is that the side that's fighting against the established Three-Domain dogma involves many of the same players that we see in other disputes. For example, that's Bill Martin on the left enjoying a cup of coffee and a donut at Tim Hortons. Another prominent critic of Three Domains is Ford Doolittle. I think the reason for this is that scientists who are knowledgeable about molecular evolution tend to recognize misconceptions about evolution and that's why they are more likely to see problems with Three Domains, opposition to junk DNA, alternative splicing, ENCODE etc.

The web of life

The importance of lateral gene transfer (LGT) became apparent in the 1990s and this led to further complications in constructing a universal tree of life. This led to an important article by Ford Doolittle in the February 2000 issue of Scientific American (see figure below). The idea is that LGT may have been so rampant in the early history of life that it's impossible to draw a universal tree that represents all the genes in a major clade. The major divisions such as archaea, eubacteria, and eukaryotes may only have emerged from the gene pool after several hundred million years.

I remember being invited to be an observer at a meeting in Halifax (Nova Scotia, Canada) in 2009 and coming away totally confused about the tree of life. (The photo is from Christina Behme at the workshop in Halifax in July 2009 on "Questioning the Tree of Life." That's me having dinner on the first evening with Ford Doolittle (left), John Dupré (standing), and Andrew Roger (right).) Now it's more than 10 years later and I still don't think there's a clear consensus of what a tree of life should look like at its deepest branches.

The popular press is just as confused as everybody else. The average science writer hasn't grasped the notion that the Three Domain Hypothesis is dead but some of them have clued into the fact that there's controversy about the tree of life. That's what led to the infamous Darwin Was Wrong article in New Scientist back in January 2009. This prompted a critical letter from Daniel Dennett, Jerry Coyne, Richard Dawkins, and PZ Myers [Blunt Talk from Four Evolutionists] but it's worth noting that three of these scientists are adaptationists of various flavors.

The tree of life is in trouble, that's the part that's right, but Darwin never said anything about what a universal tree of life should look like so, in this case, he wasn't wrong.

I'll leave you with a the words of Ford Doolittle from a 2015 interview published in PLoS Genetics [The Philosophical Approach: An Interview with Ford Doolittle].
I think there are two groups of prokaryotes: Bacteria and Archaea. They are not well defined, and there are many genes that are derived from lateral gene transfer from bacteria into archaea, somewhat fewer in the other direction. So to really say that “this bug is an archaeon” when the majority of its genes are actually bacterial, what you really mean is that you are privileging the ribosomal RNA as the definer. And that is what people do, so I will let them do that.

And then what people would believe, and I guess what I would believe, is that the eukaryotic transcriptional/translational machinery—the informational machinery in the eukaryotic cell—arose within the Archaea, more recently than the Bacteria and the Archaea diverged from each other. That would be the standard view.

But we think that a tremendous number of genes have been exchanged back and forth between bacteria and between bacteria and archaea, and also between bacteria and eukaryotes after eukaryotes arose from within the Archaea—so much transfer that it is really rather arbitrary to define these lineages by virtue of their transcriptional and translational machinery any more. Had Woese started looking at glycolysis enzymes, rather than ribosomal RNA, we might not even be talking this way.

1. There are quite a few other high-quality papers on the Two-Domain Hypothesis; for example, Williams et al. 2013. This is not meant to be a comprehensive review of all the work on this subject.

2. Another problem in these experiments arises from the use of concatenated data where a number of genes are strung together to produce a single large "gene." This is necessary because the amount of information in a single gene is not sufficient to resolve deep phylogenies. However, the individual gene trees don't usually agree with the concatenated tree suggesting that there's a problem (Thiergart et al., 2014).

Dagan, T., and Martin, W. (2006) The tree of one percent. Genome Biol, 7:118. [doi: 10.1186/gb-2006-7-10-118]

Gribaldo, S., and Brochier-Armanet, C. (2020) Evolutionary relationships between Archaea and eukaryotes. Nature ecology & evolution, 4:20-21. [doi: 10.1038/s41559-019-1073-1]

McInerney, J.O., and O'Connell, M.J. (2017) Microbiology: mind the gaps in cellular evolution. Nature, 541:297. [doi: 10.1038/nature21113]

Pace, N.R. (2009) Mapping the tree of life: progress and prospects. Microbiology and Molecular Biology Reviews, 73:565-576. [doi: 10.1128/​MMBR.00033-09]

Thiergart, T., Landan, G., and Martin, W.F. (2014) Concatenated alignments and the case of the disappearing tree. BMC evolutionary biology, 14:266. [doi: 10.1186/s12862-014-0266-0]

Walsh, D.A., and Doolittle, W.F. (2005) The real ‘domains’ of life. Current Biology, 15:R237-R240. [doi: 10.1016/j.cub.2005.03.034]

Williams, T.A., Foster, P.G., Cox, C.J., and Embley, T.M. (2013) An archaeal origin of eukaryotes supports only two primary domains of life. Nature, 504:231-236. [doi: 10.1038/nature12779]

This post first appeared on Sandwalk, please read the originial post: here

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The Three Domain Hypothesis: RIP


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