Friday, August 07, 2009

Perspectives of the Tree of Life: Day Three

Day One, Day Two

The third day (Saturday, August 1) began with a presentation by James McInerney of the National University of Ireland in Maynooth (Ireland): LUCA and LECA: Gene genesis in the genome of Eden. He examined genes in yeast cells and assigned them to ancestral homologs in bacteria and archaebacteria.

The majority of yeast genes are bacterial in origin but a significant minority come from archaebacteria. The genes with the archaebacterial origin are more likely to be found in information flow pathways (DNA replication, transcription, translation) and the genes from (eu)bacteria are more likely to be involved in other metabolic pathways.

The results suggest that the last eukaryotic common ancestor (LECA) was a hybrid formed from the fusion of a primitive bacterial cell and a primitive archaebacterial cell. The descendants of this first eukaryote subsequently entered into an endosymbiotic relationship with a proteobacterium giving rise to mitochondria and an influx of additional bacterial genes.

The second talk on day three was by Christophe Malaterre, a philosopher who divides his time between the IHPST at the Université Paris in Paris (France) and the Université Libre in Brussels (Belgium). Christophe is mostly interested in the early events in the history of life before the last universal common ancestor (LUCA) (On the roots of the tree of life). He is trying to define the basic properties of these "protocells."

This leads naturally to a debate about defining "life." During the transition from a bag of chemicals to a true living cell, there will be a zone where it will be very difficult to decide whether the protocell is living or not.

After a short break we returned to hear a presentation by William (Bill) Martin of Heinrich-Heine-Universität in Düsseldorf (Germany). His presentation was Endosymbiosis and gene transfers from endosymbionts, the most glaring insult to the tree. As the title implies, the key point is that a large percentage of nuclear genes in eukaryotes is derived from mitochondrial genes (proteobacteria) or from chloroplast genomes (cyanobacteria).

What this means is that aside from any consideration of the deep phylogeny of nuclear genes (bacterial or archaebacterial), one of the ancestors of eukaryotes is clearly a bacterial cell (proteobacteria). When you add in the bacterial contribution to genes that don't descend from mitochondria, it turns out that 75% of eukaryotic genes are bacterial in origin. No matter how you want to define the roots of the tree of life (tree, net, web) it is absolutely clear that the original Woose tree with eukaryotes on the same branch as archaebacteria is wrong!

Bill proposes that the first eukaryotic cell was formed when a primitive bacterial cell fused with a primitive archaebacterial cell. He would like to convince us that this primitive archaebacterium arose from within the current clade of Archaea. Most of us weren't convinced but none of us would dare say that to his face 'cause Bill is a very imposing man both intellectually and physically.

John Archibald of the Department of Biochemistry and Molecular Biology at Dalhousie University in Halifax, Nova Scotia (Canada) continued the endosymbiotic theme with a talk on Genetic and genomic threads in the tapestry of photosynthetic life: implications for "tree thinking."

The original photosynthetic eukaryote was the result of an endosymbiotic event involving an early eukaryotic host with mitochondria and a cyanobacterium. This gave rise to the three primary lineages: red algae, green algae, and glaucophytes. All photosynthetic eukaryotes have a single common ancestor represented by this unique endosymbiotic event.

The nuclei of modern flowering plants contain about 4500 genes derived from cyanobacteria via chloroplasts. Only half of these are targeted to the chloroplast. The rest contribute to the metabolism of the remaining part of the cell.

Some photosynthetic eukaryotes arise from a secondary endosymbiosis in which a chloroplast-containing algal cell is engulfed by a non-photosynthetic protist. In this case, genes can be transferred from the nucleus of the endosymbiote to the main nucleus, further complicating the ability to construct a treelike phylogeny that accurately reflects the true ancestral relationships of these species.

Frédéric Bouchard is a philosopher from the Université de Montréal in Montréal, Québec (Canada). When we returned from lunch we were treated to a discussion of: Endosymbiosis in light of reflections on symbiosis and the super organism.

Much of this presentation was based on symbiosis—a situation where two separate species cooperate. One or both species may benefit from this interaction and the question is how do we decide on the adaptive advantage, if any?

This was the only talk that seriously addressed the value of adaptationist thinking. Most people at this meeting seemed to assume that (almost) all evolution was due to adaptation. Bouchard even showed a slide of the Spandrels paper before going into a defense of the adaptationist program.

Andrew Roger is a former student of Ford Doolittle. He is now a professor in the Department of Biochemistry and Molecular Biology at Dalhousie University in Halifax, Nova Scotia (Canada). The title of his talk is a challenge to his former mentor: Deconstructing deconstructions of the tree of life: why a tree of microbes might be realizable, meaningful and useful.

The question is whether in light of significant LGT we can still detect the underlying vertical component in the web of life. Roger reminds us that this vertical component is very much a part of the evolutionary history of life. Let's not throw out the baby with the bath water when we question the tree of life.

There are basically two viable models of the early history of life. In the "Serious LGT" model, lateral gene transfer is ubiquitous but some genes may have been transferred less frequently than others. By looking at these genes it may be possible to recover the basic treelike vertical component of evolution.

Andrew looked at four protein encoding genes and found that they are mostly congruent with the ribosomal RNA tree of prokaryotes. The major divisions, such as cyanobacteria and proto-bacteria are confirmed. Thus, as Andrew points out, it's a mistake to assume that the web of life erases all traces of vertical descent as the alternative “Rampant LGT" model might suggest.

Almost everyone at the meeting supported the “Serious LGT" model as determined by a show of hands at the end of the day. Even Ford Doolittle raised his hand in support of his former student! (But he also supports the "Rampant LGT" model—for some reason Ford was allowed to have two votes. )

John Dupré, a philosopher at the University of Exeter in Exeter (UK) summarized the scientific part of the meeting. We are left with some important questions such as: how much does LGT compromise the tree of life? It's still an open question whether treelike thinking has to be abandoned for all of the tree of life or just for the base. The general consensus is that much of the upper regions are still treelike even though LGT may affect certain genes.

Sina Adl of the Department of Biology at Dalhousie University in Halifax. Nova Scotia (Canada) gave a short talk on PhyloCode a new classification scheme in biology. He pointed out that the current international rules of nomenclature don't work very well and need to be replaced.

The meeting closed with a talk by Susan Spath who has been with the National Center for Science Education (NCSE) in Oakland, California (USA). Her title was Cultural politics and the tree of life. Susan cautioned us to be careful when talking to the media. We should emphasize that most of the evolution that people care about (animals) is very treelike. She reminded us that talk of "Darwin was wrong" is very misleading.

As you might imagine, there was quite a good discussion on how much we should be concerned about creationists and how much we should cater to the difficulty journalists have in understanding genuine scientific controversy.

This was an excellent meeting and the organizers deserve a lot of credit for choosing the venue and the participants. It was by far the best meeting that I've attended in several decades. I plan to go to the next one in Exeter if they'll invite me back.

[Photo Credit: These photos are from Christina Behme. The bottom one is of me having dinner on the first evening with Ford Doolittle (left), John Dupré (standing), and Andrew Roger (right).]


  1. I'm one ot those that think that the archaebacterial ancestor of Eukaryotes arose from within the archaebacteria.

  2. James McInerney says,

    I'm one ot those that think that the archaebacterial ancestor of Eukaryotes arose from within the archaebacteria.

    I'm sorry to hear that.

    I won't hold it against you. I'm sure you have intelligent views on other subjects! :-)

  3. Nice summary of Day #3 - definitely worth the wait!

    I don't disagree with the Eocyte Hypothesis or whatever the newest variant is called - but it's so incredibly difficult to justify choosing one position of the Eukaryotes vs. another, given the generally messy horificness of the Archaea.

  4. Anyone talk about transfer from eukaryotes into other domains? The tRNA synthetase for glutamine is one such case (arose from a duplicated eukaryotic glutamyl-tRNA synthetase) that was transfered into a small handful of bacteria.