Culturing Science – biology as relevant to us earthly beings

Posts Tagged ‘taxonomy

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]  I’d really appreciate it! Thanks!

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

Molecular biology and globsters: dashing cryptozoologists’ dreams

This post was featured in Dave Munger‘s Research Blogging column for Seed Magazine, “Spineless But Deadly.”  Thanks, Dave!

This post was chosen as an Editor's Selection for ResearchBlogging.orgOn July 29th 2008, the day I turned 21 years, I received the best thing I could ask for: a birthday gift from Poseidon.

I was living in Newport, OR at the time.  After a long morning of observing nesting seabirds through a telescope, I returned home for what I presumed to be a long night ahead at the Rogue brewery across the street.  But I was to have more excitement first: I had gotten an email from the education director at Hatfield, informing me that 9-foot robust clubhook squid carcass had washed up on the beach just 20 miles away.  Even though I never got to see it, as it quickly made its way into an industrial freezer for preservation and future dissection, my excitement could not be quenched because obviously this was the ultimate gift from the sea (my true love).

I didn't get to see the real clubhook squid - but I did receive this lovely cake from my dear friend Lanaya the day I turned 21.

I have long had an obsession with squids, particularly of the large persuasion.  How could I not?  They are the closest thing to sea monsters that we’ve got!  They’re grotesque and mysterious, yet graceful (not really, only in my dreams — they’re actually quite slow) and sometimes colossal.  As I grew older, I realized that I was not alone, but there was a large, undefineable community of squid-lovers.  It seems to be in our nature to seek monstrosities: creatures new to science, alien, and potentially terrible.

This seemingly universal fascination and attraction to monsters is best exemplified in the phenomenon of globsters, also known as blobsters.  A globster is a blob-like animal that washes up on the shores of oceans and lakes which is morphologically unidentifiable, thus lending itself to be described as a variety of terrifying monsters as the viewer deems fit.

An early globster was the St. Augustine Monster, discovered on the coast of Florida in 1896 (a, below) by 2 young boys, originally suspected to be a giant octopus.  In 1977, a Japanese fishing trawler pulled up a hunk of flesh (dubbed “New Nessie“) (b) imagined to be an ancient underwater dinosaur, the plesoisaur, off the coast of New Zealand.  The Bermuda Blob (c) was found in Bermuda in 1988 and is the most blob-like of these three examples.  These are just three examples I chose to give here; there are more recorded examples, and many unrecorded.  (See Richard Ellis’s book Monsters of the Sea for a full history of globsters.)

Click image for larger view. Images compiled from Wikipedia.

In our modern reductionist mindset, it seems obvious what these things really are: just dead animals that have been floating out at sea, decomposing, and are thus unrecognizable by the time they wash up to shore.  But even now we are discovering hundreds of novel sea creatures every year; imagine a century ago when the sea was more mysterious and potentially dangerous.  How could a scientist identify a half-decomposed species and persuade the masses that it was not, in fact, the remains of a monster from the deep?

The answer lies in molecular analysis.  The journal Biological Bulletin published a paper in 2002 by Carr et al. identifying the the Newfoundland Blob, and another paper in 2004 by Pierce et al. looking at a variety of blobsters (including St. Augustine’s Monster, a above), but focusing on the 2003 Chilean Blob and the 1996 Nantucket Blob due to sample quality.

Both studies retrieved DNA from samples from the various blobs and sequenced their mitochondrial DNA (mtDNA).  Mitochondrial DNA is particularly useful for taxonomic identification.  It is a piece of DNA separate from your genome, found not in the cell nucleus but in the energy-producing part of the cell, the mitochondria, and is relatively well-conserved within species for easier identification.  Comparing the mtDNA sequences from their samples with known sequences from whales and sharks, Cass et al. found that the Newfoundland Blob is a decomposed sperm whale.  Similarly, Pierce et al. found that the Chilean Blob matched a sperm whale, while the Nantucket Blob was a finback whale.

Pierce et al. took it a step further and compared the amino acid compositions and microscope photos of tissue samples from many other blobsters, including St. Augustine’s Monster (a), the Bermuda Blob (c) and the 1960 Tasmanian Globster to classify those blobs as well.  They had an identical composition to the whale blubber of the Chilean blob, suggesting that these are also whale species and not large octopuses.

And thus, they’ve dashed the dreams of people all around the world who dream of sea monsters – but that was not their intent.  In fact, the authors themselves were hoping to find a new species.  Pierce et al. finish their paper with the sentence:

Once again, to our disappointment, we have not found any evidence that any of the blobs are the remains of gigantic octopods, or sea monsters of unknown species.

So do not think that the scientists are trying to say “I told you so.”  Rather, they dream big like the rest of us.

These analyses do not mean that we cannot continue dreaming; on the contrary, waterlogged animals are found regularly and each must be debunked individually.  Just this month, a strange creature was found on the shore of a lake in Northern Ontario, with a terrifying, hairless face and”creepy fangs,” covered by hair on the rest of its body.  Its discoverers suggested it was an omajinaakoo or “Ugly One,” a mythological creature considered a bad omen by First Nations (Native American) tribes.  Just this week this idea was debunked: it turned out to be a common animal, the American Mink, in a horrid state.

But don’t let these debunkings get you down.  Always keep your guard up for the excitement and horror of an undiscovered monsters.  It will at least keep you entertained.

Carr, S., Marshall, H., Johnstone, K., Pynn, L., & Stenson, G. (2002). How to Tell a Sea Monster: Molecular Discrimination of Large Marine Animals of the North Atlantic Biological Bulletin, 202 (1) DOI: 10.2307/1543217

Pierce, S., Massey, S., Curtis, N., Smith, G., Olavarria, C., & Maugel, T. (2004). Microscopic, Biochemical, and Molecular Characteristics of the Chilean Blob and a Comparison with the Remains of Other Sea Monsters: Nothing but Whales Biological Bulletin, 206 (3) DOI: 10.2307/1543636

Written by Hanner

May 25, 2010 at 7:15 am