Phylogeny Friday - 18 August 2006

Do you have any sense that Pace's little article is being considered? He raised what seemed like a number of good points.

All right, all right. Who could resist the delicate goadings of the blog formerly known as Evolgen: Blog of Destruction?

I'm not sure. I've stopped using the term "prokaryote", but that was not because of Pace's Essay. Also, I'm not in any of the fields that Pace implicates misuse terminology.

RPM says, "This tree is the accepted paradigm of the evolution of life, so there ain't much controversial here." I beg to differ. The root of the tree of life is extremely controversial. The "pure" form of the Three Doman Hypothesis - the one you show in your figure - is almost certainly wrong.

Despite great advances in clarifying the family tree of life, it is still not agreed where its root is or what properties the most ancient cells possessed - the most difficult problems in phylogeny. Protein paralogue trees can theoretically place the root, but are contradictory because of tree-reconstruction artefacts or poor resolution; ribosome-related and DNA-handling enzymes suggested one between neomura (eukaryotes plus archaebacteria) and eubacteria, whereas metabolic enzymes often place it within eubacteria but in contradictory places. Palaeontology shows that eubacteria are much more ancient than eukaryotes, and, together with phylogenetic evidence that archaebacteria are sisters not ancestral to eukaryotes, implies that the root is not within the neomura.

Cavalier-Smith T. (2006) Rooting the tree of life by transition analyses. Biol/Direct. 1:19

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The currently accepted universal tree of life based on molecular phylogenies is characterised by a prokaryotic root and the sisterhood of archaea and eukaryotes. The recent discovery that each domain (bacteria, archaea, and eucarya) represents a mosaic of the two others in terms of its gene content has suggested various alternatives in which eukaryotes were derived from the merging of bacteria and archaea. In all these scenarios, life evolved from simple prokaryotes to complex eukaryotes. We argue here that these models are biased by overconfidence in molecular phylogenies and prejudices regarding the primitive nature of prokaryotes. We propose instead a universal tree of life with the root in the eukaryotic branch and suggest that many prokaryotic features of the information processing mechanisms originated by simplification through gene loss and non-orthologous displacement.

Forterre, P. and Philippe, H. (1999) Where is the root of the universial tree of life? Bioessays 21:871-879.

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Tracing organismal histories on the timescale of the tree of life remains one of the challenging tasks in evolutionary biology. The hotly debated questions include the evolutionary relationship between the three domains of life (e.g., which of the three domains are sister domains, are the domains para-, poly-, or monophyletic) and the location of the root within the universal tree of life. For the latter, many different points of view have been considered but so far no consensus has been reached.

Zhaxybayeva O., Lapierre P., and Gogarten J.P. (2005) Ancient gene duplications and the root(s) of the tree of life. Protoplama 227:53-54.

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Rooting the 'tree of life' represents a major challenge for evolutionists. Without such a root, many of the first steps in biological evolution cannot be reconstructed. However, the nature of the last common ancestor of all living beings remains elusive, proof of the difficulty in shedding light on such an ancient event. Here, we highlight the practical difficulties and conceptual reasons that hinder the placement of a universal root.

Bapteste E. and Brochier C. (2004) On the conceptual difficulties in rooting the tree of life. Trends Microbiol. 12:9-13.

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Ford Doolittle favors the Three Domain Hypothesis but he recognizes that the root of the tree of life is still controversial.

A decade of access to whole-genome sequences has been increasingly revealing about the informational network relating all living organisms. Although at one point there was concern that extensive horizontal gene transfer might hopelessly muddle phylogenies, it has not proved a severe hindrance. The melding of sequence and structural information is being used to great advantage, and the prospect exists that some of the earliest aspects of life on Earth can be reconstructed, including the invention of biosynthetic and metabolic pathways. Still, some fundamental phylogenetic problems remain, including determining the root--if there is one--of the historical relationship between Archaea, Bacteria and Eukarya.

Doolittle, R.F. (2005) Evolutionary aspects of whole-genome biology. Curr. Opin. Struct. Biol. 15:248-53.

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Some philosophers have even begun to take an interest since the overthrow of the Three Domain Hypothesis represents an interesting shift in thinking between its overwhelming acceptance in the late 1980's to increasing skepticism in the late 1990's.

A Kuhnian framework is used to analyze the current controversy over whether two or three fundamental types of life forms exist. Until the 1980s, all life was classified into two primary forms: eukaryotes and prokaryotes. Using molecular sequencing data, Carl Woese suggested the archaebacteria constituted a third domain. In the mid-1990s, Radhey S. Gupta challenged the three-domain hypothesis. While this dispute may seem to be a purely technical debate over the analysis of protein and nucleic acid sequence data, the controversy encompasses broader issues such as the aims of classification and the role of microorganisms in the biosphere. At the heart of this dispute is what kinds of data are relevant to constructing an overall taxonomy. The prestige of molecular biology played a large role in why the three-domain hypothesis was accepted so readily, but supporters of the two-domain hypothesis argue that the fossil record, morphology, and cell physiology should all play a role in taxonomy. This case study provides a good example of a paradigm shift in the making, demonstrating that issues beyond the raw data will be significant factors in deciding whether the three-domain hypothesis will prevail or a new classificatory scheme will emerge.

Lyons, S.L. (2002) Thomas Kuhn is alive and well: the evolutionary relationships of simple life form--a paradigm under siege? Perspect. Biol. Med. 45:359-376.

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I was at a conference on this last month, and a couple of historians, including Jan Sapp, are also working on the three/five domain hypothesis. A point made often was that "prokaryote" and "microbe" and the like are privative groupings, defined by what they are not (either nuclear or multicellular), as well as being a paraphyetic group.

In the context of genetic exchange via lateral transfer I made the argument that abstractly there is a continuum of "sex" ranging from almost none (endogenous retroviral transfection) to obligate and large scale (pilus-based chromosomal transfer with mating types), and that in the context of "species" it is just the multicellular bias that makes us say that these single celled organisms lack species status.

There will be a special edition of Studies in the History and Philosophy of the Biological Sciences next year with these papers.

Phylogeny Friday is back, bitches!

I can't help but think that this expression must be off-putting to a good many of your female readers. I find it jarring, myself.

Bitch is a term of endearment. The context implies nothing insulting.

As for my assumption that the three domain hypothesis is the widely accepted paradigm: thanks for the interesting quotes. This subject is not my domain (hardy har har). The main thesis is that we shouldn't use the term prokaryote. I don't think there's much evidence for a root that causes all of the prokaryotes to become a monophyletic taxon.

RPM says,

I don't think there's much evidence for a root that causes all of the prokaryotes to become a monophyletic taxon.

Yes there is. Lots of it. Many (most?) phylogenies constructed from amino acid sequences put the first split between prokaryotes and eukaryotes if you make some assumptions. When there are gene duplications that can be used to root the tree, the root often falls between prokaryotes and eukaryotes. In many cases, the archaebacteria are parphyletic and they often group with the gram positive bacteria in the best trees. This is especially true for genes encoding basic metabolic pathway enzymes.

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