What Should We Teach About the "Tree of Life"?

As most of you already know, I think the Three Domain Hypothesis is dead. The history of life is better explained as a net with rampant transfer of genes between species [The Web of Life]. This idea has been widely promoted by Ford Doolittle.

The debate over the tree of life has implications concerning the distinction between "prokaryote" and "eukaryote." I was checking some recent papers and came across one by Doolittle and Zhaxybayeva (2013) that seems particularly relevant. They discuss the evidence for and against the division of life into three domains and the attempt by Norm Pace to ban the word "prokaryote."

The authors point out, once again, that eukaryotic genes are most closely related to genes from cyanobacteria, proteobacteria, and archaebacteria, in that order. The majority, by far, have their closest homologs in bacteria, not archaebacteria. The most likely explanation is that euakryotes are chimeras resulting from fusion of an archaebacterium and a eubacterium plus genes transferred from mitochondria and chloroplast to the nuclear genome.

Why, if the Archaeal signal is the weakest, is the Archaeal/eukaryote sister relationship enshrined in textbooks, and the concepts of paraphyly employed so enthusiastically by Pace in his effort to discredit “prokaryote”? Of course, even if the preponderance of data were all that mattered, prokaryotes would still be paraphyletic, with eukaryotes seen as sisters to the Cyanobacteria or Proteobacteria. But the more we come to see eukaryotes as a chimeric clade, established by symbiosis, cell fusion, and LGT, through the active participation of several or many prokaryotic lines, the more aptly descriptive the “eu” and “pro” in “eukaryotes” and “prokaryotes” begin to look.

Theme

The Three Domain HypothesisThey point out that biologists have a tendency to simplify and the simple Three Domain Tree of Life satisfies a natural urge.

And yet, such natural kind thinking comes naturally to biologists, generating much of the heat in our arguments. Insistence that the grade distinction between prokaryotes and eukaryotes must be discarded because it conflicts with the division of living things into clades reflects a belief that “the one true taxonomy of the universe” is the Tree of Life—to which concept, as loyal Darwinists, we feel we must cling. And yet, because of chimerism and extensive LGT, that Tree means much less as a description of what organisms are like and how they came to be that way than Darwin himself would have ever imagined (Doolittle 1999; Martin 2011).

Furthermore, the Tree unambiguously depicts three discretely defined monophyletic clades if and only if we accept as settled many highly arguable propositions about how evolution proceeds, about what the data say in that regard, and about how classification is properly to be pursued. Some of these propositions, reviewed here, are that (1) in spite of the testimony of most of their genes, the “one true” way to look at Eukarya is as sisters to or emerging from within Archaea; (2) in spite of very sophisticated recent analyses of those genes thought to be most truthful, sisterhood (rather than emergence from within) is the right way to understand this relationship; (3) Bacteria and Archaea are themselves properly described as monophyletic clades, even though it is but a few percent of their genes that tell us this, with the preponderance of genes saying that they comprise a single, albeit highly structured and admittedly very slowly mixing population; (4) that it makes sense to speak of LUCA, either as a single cell or species or (alternatively) as a heterogeneous population extended over time; (5) that it makes sense to describe LUCA (of whatever type) as something other than a prokaryote. None of these is provably wrong, but none will ever be proved right, and all are matters of opinion, not fact. Definition-dependent, supposedly logic-driven arguments on the use of “prokaryote” seem doomed to failure by the same criteria with which they are undertaken, coupled with the vast underdetermination of any of our current theories about early cellular evolution (Vesteg and Krajcovic 2011; Forterre 2011).

Most biologists haven't thought very much about this issue and that's especially true of those who teach undergraduate courses. Let's think about the ones who are up to speed. They realize that the simple tree of life is probably wrong or, at the very least, seriously misleading. Should you tell undergraduates that the history of life is a lot more messy that what they learned in high school?

Here (below) is an example of what scientists are teaching in undergraduate classes. This is a lecture by Jonathan Eisen—an expert on phylogeny—given to a class of undergraduates in the Fall of 2012. It presents the case for three domains in the strongest possible terms. Students are not told about any alternatives.¹

I ask a serious question ... is this what we should be teaching undergraduates? Is the real biology too complicated for them? Is it okay to simplify even if we know that we are misrepresenting the truth?

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1. There are very few characters that are exclusive to eubacteria and/or archaebacteria. For example, many gram negative bacteria have lipids with ether linkages and most eubacteria have DNA binding proteins that organize their DNA into complex supercoiled, looped, structures.

Doolittle, W.F. and Zhaxybayeva, O. (2013) What Is a Prokaryote? The Prokaryotes: Prokaryotic Biology and Symbiotic Associations, 21-37. [doi: 10.1007/978-3-642-30194-0_114]