Culturing Science – biology as relevant to us earthly beings

The evolution of the eukaryotes and our human story

“Taxonomy and classification are funny,” my father joked recently, “because the organisms being classified really don’t care what they are. We’re the only ones who care!”

Well, at least I thought it was a good joke.  And it speaks to a certain truth: humans generally are obsessed with organizing and putting things into categories.  It is evident in the way we divide our music into genres (“Is this chillwave or witch house?”) or put our pants in a different drawer than our shirts. This may seem silly, but, with our consciousness and perception, we need to categorize in order to make sense of our world, to generalize, and, well, to help us find things.

We no longer have unicorns in our taxonomical literature. From the Ashmole Bestiary, 1504. Via BibliOdyssey.

Long before any ideas of natural selection and evolution as we know them now, people were trying to organize the natural world around them.  In 350 BCE, Aristotle published his History of Animals, which attempted to categorize the various “natures” of animals based on their characteristics.  For example, he identified what we now know as arthropods as animals that do not have blood and, “if they have feet, have many” (French 1994).  Some of his categorizations were not so on-par; for example, he placed foxes and snakes in the same category because they both burrow underground and thus have “sympathetic natures.”  Accurate or not, the effort is there: making sense of the world through categorization.

Although we’ve been at it for a long time, we are not close to being finished identifying all extant species, much less cataloging them.  Just this week it was announced that, due to double-counts, the estimate of the number of flowering plant species will be cut by 600,000.  600,000!  And those are just the plants that are living today, excluding all the known and unknown species that have gone extinct.

It would be easy to say, “whatever, who cares about the extinct ones?  If I’m categorizing to make sense of the world, I want to pay attention to the world I’m living in.  Leave the past in the past, man!”  But if people view the world as stories as I believe we do, we need this history of organisms to construct our narrative1.

A basic illustration of the 3 domain system of taxonomy. The yellowish circles indicate the 3 nodes and the 3 domains of the Bacteria, Eukarya and Archaea. The Eukarya and Archaea share a common ancestor but evolved separately from there. Not to scale in terms of time or breadth. Drawn by Hannah Waters.

And, in particular, we need to know the history of our own species: where do we fit into the puzzle?  How far back can we trace our own ancestors?  When I was 14, I was taught that we are part of the Animal Kingdom, one of the five kingdoms of life.  When I was 17, I was instead taught the three domain system: the Bacteria, the Archaea, and the Eukarya, a classification developed by the microbiologist Carl Woese in the late 1970s.  This new system organized the world based on cell type, in particular dividing the Monera, which previously described all single-celled life, into the Bacteria and the Archaea, which are each single-celled but have many differences in structure.  (See this great post by Labrat for more information on their distinction.)  No longer were we humans described as “animals” as in ancient times, but rather based on an ancient ancestor, the first to embody the type of cell that makes up our bodies.

In the three-domain system, we eukaryotes are more closely related to the archaea, but evolved separately from a common ancestor (sister lineages).  We evolved a unique nucleus composed of specific proteins, and later acquired mitochondria or plastids from bacteria through endosymbiosis.  However, a different hypothesis has arisen in the past couple of decades: the 2-domain system.  In this system, the Eukarya are even more closely related to the Archaea.  In fact, we are a subgroup, having evolved from a singular lineage within the Archaea.  A mere secondary domain, replacing Eukarya as a “primary domain” or sister lineage as put forth in the 3-domain system.

A basic illustration of the 2 domain system of taxonomy. The yellowish circles indicate the 2 nodes and the 2 domains of the Bacteria and Archaea. Of note is that the Eukarya evolved from the Archaean domain. Not to scale in terms of time or breadth. Drawn by Hannah Waters.

Why is the 2-domain system being considered at all?  The Archaea and Eukarya share many of the same components of their genetic information systems, such as over 30 ribosomal proteins, RNA polymerases, transciption factors, promoters to initiate transcription of the genome, and replication enzymes (Gribaldo et al. 2010).  A general tenet of constructing phylogenies, evolutionary trees through time, is that the simpler answer is usually better.  Proponents of the 2-domain system argue that it is simpler for these genetic pathways to have evolved once in the older domain, the Archaea, and been retained in the newer subdomain, the Eukarya.  Proponents of the 3-domain system hold that these systems evolved earlier before the lineages split and were preserved in both the groups over time.

Eukaryotes also share many genes with the Bacteria, even more than with the Archaea.  Do these genes “even out the score” and support the 3-domain system, or were they acquired as a remnant of bacterial endosymbiosis?  An early edition PNAS paper (2010) by James Cotton and James McInerney of the National University of Ireland argues its title: “Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function.”

The authors compared every gene in the yeast genome to bacterial and archaeal genomes, finding that 952 genes have bacterial homologues, while 216 show homology to archaeal genes.  Using these genes, they performed two main tests.  First, they examined how frequently each of these genes killed the cell when deleted from the genome – a test to see just how imperative each is to the cell’s survival.  They found that lethal genes are twice as likely to be of archaeal origin than bacterial origin, giving the Archaea one “important point” in their book.  Second, they looked at how frequently these genes were actually transcribed, or copied into a form from which they can be made into proteins.  Using RNAseq, they found that there was significantly more expression of genes with archaeal homologues than bacterial.  Another “important point” for Archaea.

This study seems to support the 2-domain hypothesis: the genes that come from Archaea are used more frequently and are more necessary for cell survival, despite being fewer in number than Bacterial genes.  But remember: both systems of taxonomy support the idea that Eukarya are more closely related to Archaea.  Importance is merely a factor of correlation, not evolutionary causation.  It provides evidence that the two domains are related, but not the direct evolution of Eukarya from the line of Archaea.

These lineages have been diverging from one another for at least 2.5 billion years – it seems like a bit of a stretch to be doing genomic studies at all!  Think of all the mutations and changes that have been made in the DNA over those 2.5 billion years, obscuring the true relationships and further separating these domains morphologically.  A review coming out next month in Nature Reviews Microbiology goes through a number of studies that attempted to analyze eukaryotic evolution and found that none drew a strong conclusion, or even found conflicting results, “despite analyzing largely overlapping data sets of universal genes.”  They conclude that “it is premature to label any one of these analyses as definitive” and that these large-scale genomic studies have “not yet yielded a resolution to this debate and ha[ve], if anything, intensified it.”

Even if we did know the truth, what would this mean for the “story of human evolution” I was babbling on about earlier?  Well, it means that we’re Archaea deep down!  Those badasses who live in hot springs and sulfur!  We had the potential to be hardy, tough organisms, but instead we’re frail and get cold really easily and get hunger pangs after just a few hours…

More than anything, the fact that this debate exists in the first place gives us a great perspective on our story.  Under 2500 years ago, Aristotle categorized foxes and snakes together.  Now, we’re splitting hairs over the type of ancient cell that foxes, snakes, and ourselves evolved from over 2.5 billion years ago.  It provides the history of our progress.  And look how far we’ve come!

1 Of course there are many applications for studying evolution beyond a desire to learn about our own history.  This 2005 interview with Massimo Pigliucci, an evolutionary biologist at SUNY Stony Brook, and the 1998 collective paper “Evolution, Science and Society: Evolutionary Biology and the National Research Agenda” are good places to start.

NOTE: Molecular evolution is incredibly hard to explain (in my opinion), and I did my best to do so in English.  If you have any questions or think some parts need clarification, please let me know in the comments or write me at hannah.waters [at] gmail.com.  I’d really appreciate it! Thanks!

ResearchBlogging.org

Cotton, J., & McInerney, J. (2010). Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1000265107

French, Roger.  Ancient Natural History.  New York: Routledge, 1994.

Gribaldo S, Poole AM, Daubin V, Forterre P, & Brochier-Armanet C (2010). The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nature reviews. Microbiology, 8 (10), 743-52 PMID: 20844558

Written by Hanner

September 29, 2010 at 7:52 am

12 Responses

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  1. […] This post was mentioned on Twitter by Andrew Thaler, Hannah Waters. Hannah Waters said: New post at Culturing Science: The evolution of eukaryotes and our human story http://bit.ly/aaAyAJ […]

  2. I completely agree that Archaea are neglected by current intro bio textbooks – a point that I have been making with textbook editors, to little avail thus far. Thanks for this post – I will direct my intro bio students to this. One correction: archaea and eukarya diverged 2.5 billion (with a b) years ago, not 2.5 million (with an m) – but what’s a factor of 1,000 between friends?

    Jung Choi

    September 29, 2010 at 9:58 am

    • WHOOA!! Thanks for the catch, haha. Indicative of my late-night writing style, I think. Dave Munger wrote a SEED column today on Archaea, “The Forgotten Domain,” which I highly recommend for more Archaea lovin’.

      Hannah Waters

      September 29, 2010 at 10:02 am

  3. Thanks for the linkback! Good stuff and I love the little handdrawn pics, should start doing more of those myself XD. Archaea have been getting quite a lot of press lately which is nice to see.

    The two domain system is very interesting. I had heard of people saying that archaea were more related to euks and bacteria were but I didn’t realise it had gone that far!

    Lab Rat

    September 29, 2010 at 11:04 am

  4. Great post. Still, I wonder how the ring of life model fits into the picture.

    Igor Topilsky

    September 29, 2010 at 1:03 pm

  5. […] The evolution of the eukaryotes and our human story […]

  6. I’m not a biologist but currently studying astrobiology rooted in Earth biology as a type case – and I don’t recognize much of the later here.

    we need this history of organisms to construct our narrative

    Narratives are meaningless unless they are used by persons to construct their personal meaning. Which is a rather odd way of doing that as there are much better ways congruent with science knowledge. And in science we need facts, not the exact opposite.

    A basic illustration of the 3 domain system of taxonomy.

    No. The basic 3 domain system is unrooted, with the 3 branches as topological equals. Woese himself was rather convinced that original massive lateral gene transfer had unrooted and transformed the tree to a genetic “melt”.

    What you are showing is a phylogenetic tree rooted within bacteria, with euks and archs as sisters.

    This is pretty much what modern cladistics points to when they combine multi-gene phylogeny with transition analysis. (Actually, last year multi-gene methods arrived at the sister relationship that Cavalieri-Smith predicted earlier from traditional phylogenetic methods, only barely so.)

    However, a different hypothesis has arisen in the past couple of decades: the 2-domain system.

    I’ve never heard of the term. But the hypothesis that the euks were endosymbiotic descendants of an arch/eubacteria event is older and uncoupled from the over all tree.

    These lineages have been diverging from one another for at least 2.5 billion years – it seems like a bit of a stretch to be doing genomic studies at all!

    No. Single genes may have been diverging for that long (disputably, since there are long branch attraction effects and other effects messing up timing) but the populations themselves are (whole genomes) diverging much later.

    There are two reasons to think that the arch/euk split is a third that age, perhaps ~ 1 Ga at most.

    First, archaea is one of the few clades that mostly does well with single (rRNA) gene trees. The near absence of long branch attraction means it is a young and fairly uneventful clade.

    Second, easily recognizable eukaryote cells are also young and don’t show up in the fossil record until that age. People used to point to steranes, the breakdown products of sterols, as older eukaryote molecular fossils. But they are produced by a couple of eubacteria clades as well, and the existence of a well-defined tree now implies that the genes likely originated there.

    Torbjörn Larsson, OM

    October 2, 2010 at 6:02 pm

  7. Also, it should be noted that the predictions from the sister hypothesis is independently tested by the recent discovery of endomembrane proteins and endocytosis in Planctomycetes, especially the yeast like nucleus/budding behavior of G. obscuriglobus. These bacteria may be descendants of the ancestors to arch/euks, and if so resolve the chicken-and-egg problem of endosymbiosis. Even if they aren’t, they show that endomembrane proteins are older. (Again, with the support of the observed tree, depressing lateral gene transfer as likely pathway.)

    In fact, it holds out the exciting possibility of undiscovered endosymbiotic events outside the euks!

    Torbjörn Larsson, OM

    October 2, 2010 at 6:15 pm

  8. “Narratives are meaningless unless they are used by persons to construct their personal meaning. Which is a rather odd way of doing that as there are much better ways congruent with science knowledge. And in science we need facts, not the exact opposite.”

    Science is all about stories. Most things people do are all about stories. Narratives are not meaningless to humans, and it is humans doing the science.

    Lab Rat

    October 5, 2010 at 10:38 am

  9. Hannah, you have drawn the cladogram of the new hypothesis as if the Archaea are paraphyletic. Is that actually suggested in either paper? Otherwise, if Archaea would still be monophyletic, then the difference in the trees seems rather inconsequential, merely being that the common ancestor was an Archaean, which is not at odds with the 3-domain tree.

    No. The basic 3 domain system is unrooted, with the 3 branches as topological equals. Woese himself was rather convinced that original massive lateral gene transfer had unrooted and transformed the tree to a genetic “melt”.

    Torbjörn, I am not sure what sense this comment of yours/Woese’s make. The 3-domain system has been rooted, contrary to what you say. The rooting is in doubt, with some even suggesting that it should be put at the Eukaryote branch (Philippe and Forterre, J Mol Evol (1999) 49:509–523). There were very probably lots of LGT going on back in the beginning, but that does not mean that there is no rooting possible, just that it’s very hard for us to do it.

    Bjørn Østman

    October 31, 2010 at 10:46 pm

  10. Well, it means that we’re Archaea deep down! Those badasses who live in hot springs and sulfur! We had the potential to be hardy, tough organisms,

    Ahhh, but we are! We’re extremophiles: we thrive in an Oxygen-rich atmosphere that was poisonous to many/most organisms when it developed (and still is, to many). It’s ‘home’ to us, just as a hypersaline hotspring is to some groups…

    but instead we’re frail and get cold really easily and get hunger pangs after just a few hours…

    Only we homeotherms; a consequence of maximizing (oxidizing) metabolic rate. As for “get cold”; think of what a hyperthermophile would “feel” if introduced to our living room…

    p.s. you need a ‘preview’ button

    djlactin

    November 2, 2010 at 12:20 am

  11. […] wrote for Hannah from the award winning blog Culturing Science. She writes great posts on ecology, evolution and science (communication) itself, so go and check out some of her […]


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