The official blog of University of Missouri Skeptics, Atheists, Secular Humanists, & Agnostics

A Poorly Illustrated Guide to the Tree of Life: Part 2

Hello again, Dear Reader. I hope you enjoyed reading Part 1 as much as I enjoyed pretending I didn’t write it; if not, please go back and read it again and again until my words become like a fine spiced beverage soaking through your brain. Also, reading Part 2 without the benefit of context will probably render my already muddled narrative wholly incomprehensible. You’ve been warned.

Part 2: Animals are Confusing: Sponges and Choanoflagellates

Now that we know what an animal isn’t, how do we move forward? As promised in Part 1, there are actually traits joining all animals in a nice clean monophyletic taxon, and they shall be presented herein.

This flow chart made more sense right after I drank all that absinthe.

Well, the taxon isn’t actually so nice. Or clean. In fact, the line between true animals and not-quite-animals gets quite murky, as we shall soon see. However, fear not, Dear Reader: Although things may get rather messy, the rain-scented, foaming-action of phylogenetics and molecular biology will probably save the day.

But first, let’s talk about our good friend, the Sponge!

This is a sponge.

This photo-realistic image depicts one of the sea’s most familiar denizens. Proud, noble, and perhaps mildly arousing, the sponge has quite an impressive history of scrubbing grimy Ancient Greeks, absorbing many an unsightly puddle, and inspiring today’s youth. Yes, I hardly need shower accolades upon the sponge, so great has been its contribution to humanity. So why have I decided to digress and take up valuable your-mother joke space discussing their merits? Sponges straddle the line between different types of organism; they are asymmetric, largely amorphous, and altogether alien to land-dwellers like us. There’s nothing quite like them, and a brief look at sponge biology will inform our understanding of what makes an animal.

Kitchen sponges don't contain any actual sponge; not since the Great Sponge Aggression of the '78.

Their habitat spans all the world’s oceans wherever sediment-free water is found; from pole to pole, along the coasts, down continental shelves, and across the ocean floor to the abyssal depths. A few species can even be found in freshwater environments, including everybody’s favorite continental rift lake: Lake Baikal.

The slightest pretext to draw Eurasian bodies of water is all I need.

The sponge body plan is quite variable, ranging from inconspicuous crusts to gigantic barrel-shaped cylinders. Internally, sponges are, for lack of a better word, untidy. Most of the sponge’s body is composed of a non-cellular gel, called the mesohyl, and some kind of scaffolding material.  The exact composition of this scaffolding is variable (including silica spikes called spicules, protein fibers, and several forms of calcium carbonate) and is important in the classification of the major types of sponges. These two substances are collectively known as the extracellular matrix, or ECM.

A sampler of some example sponge body plans: potbellied (left), sad cactus (center), and bluish amalgam (right).

Sponges lack anything readily identifiable as proper organs or organ systems, although a cross-section reveals an extensive network of hollow spaces that I’m willing to call organs if you’re willing to call the blackened space within my chest a heart. In the typical sponge, these channels begin as small tube-shaped cells (porocytes) along the external surface of the sponge and gradually expand into a series of increasingly spacious chambers until reaching a large central cavity, which ends in a terminal vent, called the osculum. This system serves three important functions: feeding, material exchange, and reproduction.

I couldn't agree more, Mr. Fish. 1. Water and food particles enter through a pinacocyte (not shown); 2. Water then enters the central chamber and is filtered by choanocytes; 3. The water finally exits through osculum; 4. All the while, nutrients are dispersed into the mesohyl.

Understanding how the sponge works its magic requires a close look at the cellular level. There are two very broad types of cell in sponges; external and internal. External cells line the parts of the sponge in direct contact with the surrounding water, including the previously mentioned hollow channels. Internal cells are embedded within the jelly and fibers that make up the actual sponge body.

A very rough map of sponge cell types in relation to the environment. A very, very rough map.

External cells can be further divided (Yay, isn’t biology fun?) into protective skin-like epithelial cells called pinacocytes and fancy flagellated cells, known as choanocytes, that line the channels. Like all true gentlemen cells, choanocytes wear a ruffled Victorian collar of cilia around their stately flagella visages. The choanocytes spin and flex their flagella to generate tiny water currents inside the sponge interior, pulling in fresh water, food particles (mainly bacteria, algae, and plankton), and, somewhat disturbingly, sperm; all the while expelling dissolved waste products out of through the osculum.

A single choanocyte embedded inside mesohyl (yellow). The flagellum (light blue) wiggles like an excited kitten tail, pushing water and food particles through the collar of cilia whiskers (dark blue). Food is captured by the cilia, carried down to the cell body, absorbed as a vacuole (i.e. phagocytosis), and digested in the cytoplasm.

There are several types of internal cells with subtly different functions, including cells that secrete materials (such as collagens, polysaccharides, and silica), facilitate changes in shape (sponges can actually contract and shift position, albeit slowly), produce gametes (them’s sexy-time cells), and act as a primitive immune system that attacks and engulfs foreign particles. Internal cells are generally amoeboid in shape, and their functions can sometimes overlap. The sponge equivalent of a stem cell is the totipotent archaeocyte, which can mature into any cell type.

A close up view of a slice of delicious sponge cake: 1. Pinacocyte; 2. Porocyte; 3. Secondary Chamber; 4. Mesohyl with Spicules; 5. Archeocyte; 6. Choanocyte; 7. Inner Chamber.

True tissues, defined as ‘a part of an organism consisting of an aggregate of cells having a similar structure and function’ and derived from a common cell lineage are generally believed to be absent from sponges; an understandable yet misinformed belief resulting from the erroneous notion that sponges are simply a chaotic heap of primitive organic material. Although certainly lacking the localization of vital functions found in most ‘higher’ forms of life (breaking a sponge in half effectively creates two perfectly happy new sponges), the various layers of cells are structurally and developmentally similar, well organized, and only function by virtue of their spacial arrangement. If that doesn’t qualify as a tissue, I’d venture to say that there exist no true tissues in biology. Different individual cells, especially the external type, appear physically joined to one another in a variety of configurations similar to those of higher multicellular organisms. Indeed, sponges resemble us sophisticated animals in more ways than that.

A Venus' Flower Basket sponge, Euplectella aspergillum, here looking like some kind of poorly rendered black tornado. These are almost cool enough to warrant looking at an actual picture... almost.

Sponge reproduction is a sordid and lusty business, and can take place either sexually or asexually. Each individual sponge is hermaphroditic, producing both sperm and egg cells. Sperm are ‘broadcasted’ (a subtle euphemism for penis-less ejaculation) out of the osculum of one sponge and absorbed by the inner cells of a different individual, where they are transported to an egg. Kinky, right? The fertilized zygote develops into a sphere of undifferentiated cells, a blastula, which in turn develops into a ciliated embryo that may be retained within the sponge or released into the water. Asexual reproduction involves the production of a detachable structure, called a gemmule, made of a mass of archeocytes surrounded by a protective envelope. The gemmule floats away, settles on a substrate, and the archeocytes multiply and diversify into the various cell types, producing a miniature adult. This development is accomplished thanks to the sponge’s complement of regulatory genes, called homeobox genes. These act like genetic switches, turning other genes on and off in different part of the sponge and at different times.

Sponge sex is hotter than one might expect.

I know what you’re thinking, “Wow, thanks for teaching me about sponges. I always wanted to know about porocytes and oscula and sperm or whatever. But tell me: What does this have to do with animals?” Your concerns are duly noted, but before I get to that, please take a look at another critter for seemingly no reason:

A single choanoflagellate in all its glory.

This little darling is a single-celled aquatic organism known as a choanoflagellate. These fellows spend their days flapping their long central flagella round and round, generating tiny water currents that pull food particles into a ring of basal cilia and circulate gasses while expelling waste.

A collared, uniflagellated cell that captures edible material from the surrounding water? Now why does that sound familiar?

Remember me?

Oh yeah!

The structural and functional similarities between choanocytes and choanoflagellates are more than just an artifact of my poor illustrating abilities: Microbiologists have noticed the uncanny resemblance between these two organisms for well over a decade, and only the most experienced are able to tell the two apart in vitro. Perhaps the most intriguing aspect of this relationship is the existence of a number of colonial choanoflagellates. These colonies can consist of a simple string of neighboring individuals attached at the midsection to spherical structures possessing multiple cell types suspended in a sponge-like gel matrix.

A few different colonial forms of choanoflagellate. The most recent common ancestor of all animals may have been similar to a creature similar to one of these.

Finally, we return to our discussion of animals. What are the shared characteristics that unite all animals into the Kingdom Animalia and distinguish them from all other living organisms? If you’ve read the entire article up to this point, then you may be surprised to learn that you already know what those features are. That’s right; and you thought I was just wasting your time with sponge-related nonsense. Sponges are animals; in fact, they make up the oldest linage of extant animals (actually lineages, but I’ll get to that). Choanoflagellates are not animals, but are closely related to sponges. Presumably, the differences between the two groups should illuminate what qualifies as a uniquely animal trait.

Being an animal depends on possessing 4 shared characteristics that were present in and derived from the most recent common ancestor that all animals share; features meeting this definition are known as synapomorphies. Precursors to these 4 traits have been located in other organisms, consistent with the gradual process of evolution, but their particular metazoan functions evidently evolved only once and are represented to some degree in modern sponges. Keeping with conditions (1) and (2) as laid out in Part 1, these 4 characteristics (1) describe all animals, and (2) describe only animals.

1. Blastular development:

At some point during the embryonic development of all animals, there is a stage where the cells form a hollow sphere, the blastula. This structure plays an important role in the formation and growth of animal germ layers. In sponges, the blastula generally drifts in the water column, directed in some limited capacity by its ciliated surface.

2. Metazoan multicellularity:

There are several groups of multicellular organisms; true plants, fungi, some bacteria, and a variety of protists (i.e. slime molds, seaweeds and other algae); however, the particular way animals achieve multicellularity is unique and readily identifiable. Metazoans possess a number of cellular junctions and attachment structures not found in other groups, facilitating everything from selective permeability of organs and body cavities to cell-cell communication.

There are three broad classes of animal cell junction: occluding, adherens, and communicating. Occluding junctions allow sheets of cell to form impermeable or semipermeable membranes. Adherens junction are the cellular equivalent of bolts, fastening cells to one another using proteinous bits of the cytoskeletion. Desmosomes and hemidesmosomes are chief among these, binding cells to other cells and the ECM, respectively. Communicating junctions, as you might expect, facilitate cell-to-cell communication (think neurons and the like). Plants and fungi have similar structures (the plasmodesmum in plants and septate junctions in fungi) that allows two cells to trade cytoplasms and other substances, but they are evolutionarily unrelated to those of animals.

Sponges don’t rely heavily on junctions to achieve their multicellularity. Although rudimentary, some sponge cells are connected in the distinctive metazoan configuration (including some desmosome-ish structures in pinacocytes). Choanoflagellates possess many of the same genes used by animals to attain multicellularity, but they don’t provide the same function; indicating an important evolutionary change in the shared common ancestor of all animals. Communicating attachments (gap junctions and synapses) aren’t known in sponges.

3. Extracellular matrix:

Lacking the ridged cell walls found in other creatures, animals rely heavily on secreted, non-cellular materials for structure and cohesion. The most ubiquitous of these materials is collagen, a protein found in great abundance in both sponges and most other animals. These fibers link together and into a lattice, serving as an anchor for surrounding cells and other neighboring extracellular matrix. Like those involved in multicellularity, sponges and choanoflagellates share many of the genes, but their specific functions differ significantly (although the colonial forms of the latter may represent a significant exception).

4. Structural regulatory genes:

Animals, being relatively complicated things, require some special instructions for building their bodies. These instructions are encoded in special genes called homeobox genes. These genes are translated into a specific kind of protein, regulatory factors, that bind to other genes in the genome and regulate whole groups of other genes responsible for growth and development. Metazoan homeobox genes come in a few different flavors, the most well studied being Hox genes (homeobox genes are found throughout eukaryotes and aren’t unique to animals, but Hox genes are). Hox genes are responsible for the segmentation observed in many animals, and even have a tendency to be spatially arranged in the proper order on the chromosome. Sponges appear to lack true Hox genes (unsurprising considering their lack of segmentation), but possess a related class of regulatory genes known as NK genes. NK genes are not exclusive to metazoa, but there is compelling evidence that they are the progenitors of true Hox genes. All of these observations make structural genes a somewhat tenuous and arbitrary synapomorphy; I present it here because it works with a little bit of imagination.


These 4 traits are present, in some form, in all animals; including our spongy friends. Although sponges and choanoflagellates are very similar, sponges are more closely related to all other animals than they are to choanoflagellates, which are not animals but are just outside the Animalia clade (also referred to as the clade Metazoa). In fact, choanoflagellates are the most closely related group of non-animals to the metazoans (the two groups actually form their own clade, Filozoa), and the hypothetical proto-animal ancestor of all animals was probably similar to modern choanoflagellates. If you take a few evolutionary steps backwards, it turns out animals and their other Filozoan brethren share a common ancestor with the fungi. This group, collectively called Opisthokonta, is defined by the synapomorphy of a single posterior flagellum (in case you’re wondering where your posterior flagellum is, you lost it once your paternal half stopped being a sperm cell and became a zygote). This nested hierarchy of taxa and traits has some very significant evolutionary implications (and makes a mockery of the tired notion of the ‘common design, common designer’ argument creationists are so fond of putting forth to explain the unity of form shared by all earthly organisms), and the recently sequenced genomes of representative sponges and choanoflagellates is shedding light on the evolutionary origins of multicellularity, genetic regulatory mechanisms, connective proteins, immune systems, and embryonic development.

A phylogenetic tree of the Domain Eukaryota made of that scientific gold I was talking about earlier. Emphasis is placed on the Opisthokonts, the large blue taxon. The creatures in the 'etc...' group include fungi, slime mold, and lots of other weird and unspeakable thing: If you exclude this group, you've got the clade Filozoa (light blue). Excluding the choanoflagellates yields the clade Metazoa (slightly lighter blue).

You might remember a third condition from Part 1: All animals must ‘consist of a monophyletic grouping of creatures united by common ancestry.’ Does the Kingdom Metazoa, as described here, actually represent a group fitting condition 3? After all, a collection of very similar organisms can be incredibly similar morphologically, behaviorally, ecologically, and cellularly while still being the result of convergent evolution rather than recent common ancestry.

For example, take these creatures:

Remember us?

That’s right: Sponges! Has your brain liquefied from astonishment? Sponges, the very paradigm of biological integrity, do not qualify as a valid evolutionary clade (these animals were formerly placed in their own phylum, Porifera; a term I’ve avoided using until now on account of its dubious status). The 3 or 4 major assemblages of sponges form genetically distinct taxa whose most recent common ancestors are nearly as old as the Kingdom Animalia itself. One of these groups, Hexactinellida (glass sponges like the Venus’ Flower Basket), is probably the oldest. Another, Homoscleromorpha (the bluish amalgam illustrated above) , may be the sister group to the rest of the Metazoa.

I’ll address this vexing topic, as well as provide evidence that Metazoa meets condition (3), in Part 3. Until then, enjoy this final illustration and these fine references:

A highly simplified phylogeny of the Eukaryotes. Animals and Fungi (as well as choanoflagellates, slime molds, several kinds of amoebae, and a few other protists that don’t quite fit into those two groups) unite to form the monophyletic taxon Opisthokonta. Plants (and their algal friends) represent a sister group.

Carr, M., Leadbeater, B.C.S., Baldauf, S.L. (2010) Conserved Meiotic Genes Point to Sex in the Choanoflagellates. Journal of Eukaryotic Microbiology. 57(1)
Fahey B., Larroux C., Woodcroft B.J., Degnan B.M. Does the high gene density in the sponge NK homeobox gene cluster reflect limited regulatory capacity? (2008) The Biological Bulletin. 214(3)
Gazave, E., Lapébie, P., Renard E., Vacelet, J., Rocher, C., Ereskovsky, A.V., Lavrov, D.V., Borchiellini, C. (2010) Molecular phylogeny restores the supra-generic subdivision of homoscleromorph sponges (porifera, homoscleromorpha). PLoS One. 5(12)
King, N. et al. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. (2008) Nature. 451
Lang, B.F. et al. (2002) The closest unicellular relatives of animals. Current Biology. 12(20)
Nielsen, Claus. Animal evolution: interrelationships of the living phyla. (2001) Oxford University Press, New York. 2nd Ed.
Snell, Elizabeth et al. (2001) Hsp70 sequences indicate that choanoflagellates are closely related to animals. Current Biology. 11(12)
Valentine, J.W. On the Origin of Phyla. (2004) University Of Chicago Press. Chicago.

James is a graduate of the University of Missouri, Columbia. He is a research biologist specializing in the molecular evolution of invertebrates. Feel free to visit his subpar research blog.


3 comments on “A Poorly Illustrated Guide to the Tree of Life: Part 2

  1. Cade
    November 23, 2011

    I can’t believe you don’t have any comments yet, so I’ll leave one. Great work! Reminds me of ‘Hyperbole and a Half’, but for Biosci nerds. As one such nerd, I applaud your effort. I’ll leave you with a specific complement and criticism. Aside from your art being spectacular, I really enjoy the way you frame your discussion of animal life around sponges and choanoflagellates. It’s really quite clever, and makes a clear case for what defines an animal. On the other hand, your paragraph describing metazoan multicellularity is a vague little blurb of nothing that does little to describe exactly what makes animal multicellularity unique. Plants and fungi are also multicellular, as any reader who finds this blog should know, and there’s nothing in that paragraph to suggest what the differences are. Also, if you draw a diagram of the way fungal multicellularity looks, I might love you forever. That shit is weeeeeeird.

    • jmpd36
      November 23, 2011

      Thanks for the comment! I really appreciate your feedback, and especially your criticism.

      To address that criticism: I totally agree! I’ve yet to mentally digest everything about metazoan multicellularity into a form I can readily dispense in a clear way, so that part is a bit more black-boxy than I’d like. There are a number of distinctly animal cell junctions (gap junctions, desmosomes, triple junctions, etc.), but where they turn up on the metazoan tree varies greatly (and some, like the desmosomes, show up in plants, albeit as a homoplasy). Then you get into sponges, which have some odd ways of expressing multicellularity, including the glass sponges which are basically one giant enclosed mass of cytoplasm with millions of nuclei floating around. On top of all this, the genetic basis for all these structures isn’t well understood yet (at least to me). This prompted me to include multicellularity (as its unique origin in animals is a good synapomorphy), but to punt on the details to avoid getting something horribly wrong… although I suppose I could have posted what I just wrote here… I might have do that.

      tl;dr: Multicellularity is tough, and I’m not very smart =D

      And fyi, I’ve also got a soft spot for mycology, so expect some fungus-related content in the near future.

  2. Pingback: A Poorly Illustrated Guide to the Tree of Life: Part 3 « The Official MU SASHA Blog, Updated Daily

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s


This entry was posted on November 23, 2011 by in Author: James Cook, Science.
%d bloggers like this: