"Just another ciliate" – importance of sexy descriptions

There are species descriptions, and then there are species descriptions. All too often, you come across a mention of some obscure but ridiculously cool-looking organism, with only a very scant description of what it looks like and what it does. Much less often, you can come across yet-another-new-species (usually of a ciliate), but a particularly nicely described one. Again, those super nice descriptions tend to be of ciliates, largely due to the likes of Wilhelm Foissner and his academic offspring. Descriptive detail can only make species more interesting, and eventually of great potential to be useful for science. (Conversely, many a taxon has been rendered invalid due to poor description)

A sexy description is also a great way to lure readers into noticing your otherwise garden variety new species. Case in point – I see this random IJSEM paper on a couple new marine ciliate Frontonia species – nothing too earth shattering. Being rather compulsive about skimming over any mention of a protist I see in the literature, I click. Being rather lazy and a shallow-minded picture-loving type, I head straight for the figures. Unexpectedly, they dazzle me with sexiness. Desperate for something easy to blog about for the next little while (impending interview, exams, end-of-term chaos, etc), I suddenly find your otherwise-routine new species description quite exciting and blog about it. Here, Frontonia mengi and F.magna get screentime largely thanks to their authors.

Some of us in science are that simple minded. If more people realised that and preyed upon our ilk with shiny pictures, think how much more presentable science as a whole would be!

(That said, no amount of gloss and shine can make your data more or less wrong. But it can, and does, dazzle some of us into overlooking a flaw or three...)

Actually, the above was just a long-winded elaborate excuse to post ciliate porn. Ah, check out the kineties on that ass!

Frontonia mengi. See text. (Fan et al. 2010 IJSEM)

Well, those were mostly just shots of its oral ciliature, but close enough. The root structures of the cilia are highlighted with silver nitrate and carbonate staining, yielding the pretty staining effect. a-c section through the 'mouth'; d shows the "membranelle" around the 'mouth'. e shows the area behind the mouth; arrowhead points to the cytopyge. 'Cytopyge'? Well, a cell's gotta get rid of its waste somehow, and ciliates actually have the cellular analogue of an asshole. Not the socially dysfunctional kind. So yeah, look at that ass. g shows detail of the cortex, h is the overall view of the ventral ciliature. At i, the rows of cilia "stitch together" at the 'anterior suture'. k shows the germline micronucleus (Mi) and somatic macronucleus (Ma).

Now for some delicious DIC:

Frontonia mengi. See text. (Fan et al. 2010 IJSEM)

Crisp DIC intoxicates me. The seductive allure of polarisation-derived faux-3D relief is nearly impossible to resist, especially when you have the fine complex cell of a ciliate. In fact, good DIC is often better than staining, since you don't have to fix (kill) anything. Unfortunately in the case of some larger ciliates, some degree of squishing must be done otherwise the sample is too damn thick for crisp DIC. I think the gist of microscopy can be summarised as the never-ending compromise between care of specimen and care of the optical setup. The most powerful microscopy generally requires total destruction of the specimen, whereas the most natural and undisturbed data can only be attained with simple techniques and weak optics. It's like the Heisenberg principle of microscopy: the more accurately you determine the state of your specimen, the more mangled your specimen gets.

I digress. In the above plate, a-e show general views of several individuals of F.mengi. Remember my rant a couple posts ago about the usefulness of depicting morphotypical (shape type) variation? I hope it is evident here how that can be useful. For example, if only figure a was published, one could be mislead to consider that large vacuole a characteristic feature of this particular ciliate species. The other four images, however, show that to be a feature of just that specimen instead (non-contractile vacuoles, in this case). Furthermore, the authors even invluded a table of morphometric data, measuring the body dimensions and some visible subcellular details (like numbers of kineties and nuclear size) of 23 individuals.

The arrow in 1b points to a contractile vacuole – one could just make out the channel leading to the cell's exterior for expelling its contents. f-g show sections of the mouth, live. h shows detail of the cell surface, the oral apparatus quite visible (as is the cytopyge). i details the cytopharyngeal rods, which are specialised structures this genus of ciliates employs to devour long strands of algae. The characteristically massive ciliate nuclei are visible in j – the arrow points to the macronucleus while the arrowhead points to the micronucleus. No staining necessary, fuck yah.

Frontonia, like many ciliates, is also armed and dangerous. The surface is loaded with extrusomes (k), which can fire leaving a trail, much like the cryptomonad ejectisomes (l). m and n show the contractile vacuole and its exit pore, respectively. The contractile vacuole is necessary for osmotic regulation, especially in freshwater species, and is somewhat analogous in function to our kidneys.

The second species, Frontonia magna, is also well-described. In these specimens, one can make out the algal filament and its constituents – particularly in b, e and f. Like F.menga, it's also loaded with extrusomes (h). I particularly like i, which shows the ciliature of the anterior suture. It's quite hawt.

Frontonia magna. See text. (Fan et al. 2010 IJSEM)

Of course, no description is properly complete (in my opinion) without drawings to accompany the micrographs. Drawings highlight the important features observed by the authors, and are useful in combining information gathered from multiple sections and imaging techniques in a convenient summary. Making an accessible visual summary of a huge pile of microscopy data is no easy task, and is very much an art.

Continuing with F.magna, a summarises the ventral view of a typical individual. b provides a sketch of the sutures, without the distracting detail. c shows the side view, along with the contractile vacuole. d shows the relative sizes and positions of the nuclei. e, again, emphasises variation – it shows the various ways a cell appears after overeating with algal filaments protruding all over the place. It's amazing how hard prey can try to make their predator look like an entirely new freaking domain of life, by stretching it out and colouring it in all sorts of funny ways. A similar phenomenon has been responsible for an entire mistaken genus, Ouramoeba, in the otherwise totally awesome Leidy 1874 work on amoebae. The algal prey is detailed in g, while h details the cilia around the oral apparatus.

Frontonia magna See text. (Fan et al. 2010 IJSEM)

Of course, no species description these days is complete without a healthy phylogeny, and Fan et al. got that covered too. I feel I've stolen more than enough figures already, so I'll just say their Frontonia spp. fit snugly within Peniculia, a group including the famous Paramecium, and the two species are sister to each other. There's also a composition of drawings from multiple sources for other members of this genus, so this paper is a nice current reference for Frontonia, if you ever wake up one morning needing one. Believe me, these cravings may strike at the oddest hour.

Anyway, I just thought these figures really deserve to see the light of day, and not just remain buried away in what will very soon be just the back issues of a microbial systematics journal. While some may look down on routine-seeming research like basic species descriptions for they do not provide a fancy high-level synthesis or anything, but ultimately, these fancy high-level syntheses are built on lower-ranking papers like these, and cannot exceed the quality of their constituents. It is primary 'basic' literature like this that forms the foundation of science; without species descriptions, without "yet another gene/genome/tree/whatever", there will be nothing to base the more glamorous studies on. This is why impact factor is a load of bullshit, and anyone whose hands itch to oppress "low impact" science should be kept the hell away from research funding strategies, for they obviously have no fucking clue how research works in the first place. Grrr. How can anyone vote against a species description as awesome as Fan et al. 2010 above?

Reference
Fan, X., Chen, X., Song, W., Al-Rasheid, K., & Warren, A. (2010). Two new marine Frontonia species, F. mengi spec. nov. and F. magna spec. nov. (Protozoa; Ciliophora), with notes on their phylogeny based on SSU rRNA gene sequence data INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY DOI: 10.1099/ijs.0.024794-0

Sunday Protist - A sampling of Cercozoa Part I

This post grew out of proportion, so I'm splitting it into two or three parts, to cater to our ever-shortening attention spans (mine included)...

[Warning: Taxonomy. Of the harshest kind: involves Cavalier-Smith]

At the moment, among my favourite supergroups is Rhizaria (tree). Rhizaria is generally where all the obscure, interesting, and outright weird eukaryotes get sent by molecular data these days. The group itself is fairly recent, having been formally spewed out declared by Cavalier-Smith in 2002, as a fusion of Cercozoa and Retaria(=forams and 'radiolarians'), as well as Heliozoa and Apusozoa, apparently because they had "a centrosomal core or radiating microtubules and two microtubular roots and soft surface, typically with reticulopodia." (TC-S 2002 IJSEM:297) Don't worry, I don't really know what that means either. That is, those are fairly common traits in many non-Rhizarians, even according to the TC-S 2002 classification.

The name derives from the group's inclusion of many members of the then-defunct "Rhizopods" ('root-feet' - members typically had thin, branchy pseudopodia). Since then, Heliozoa died a horrible death with its limbs strewn all over the tree (Nikolaev et al. 2004 PNAS) and [many] Apusozoa now seem to enjoy their privileged life as the putative basal Opisthokonts (or their sisters). Ironically, many of the "Heliozoa" did return to Cercozoa later. Obligatory TC-S Diagram:

The birth of Rhizaria. As the young supergroup struggles to open its eyes to the world for the first time, it is confronted by the glaring faces of frustrated readers threatening to ban the author from ever birthing another taxon, for the sake of global sanity. Yet, despite its weak, fragile synapomorphies, the newborn supergroup, heavily-medicated by state-of-the-art molecular phylogenies, rises to become a bona fide citizen of the taxonomic world. For now. As all other life forms on earth, the higher taxa themselves are mortal. (diagram slightly modified (red box added) from Cavalier-Smith 2002 IJSEM)

"Radiolarians" (Acantharians+Taxopodids+Polycystines) and Forams (more generally, Granuloreticulosea) are massively diverse, complicated and awesome, but Cercozoa are more obscure to non-protistologists, and are a rather weird assemblage of stuff. I think the Amoebozoan taxon "Variosea" would have been quite fitting for them, were it not taken by amoebae instead. Cercozoa is older than Rhizaria, but not by much - it was formally established by Cavalier-Smith in 1998 (Biol Rev) as a modified successor of Rhizopoda:

"The recently revised phylum Rhizopoda is modified further by adding more flagellates and removing some ‘ rhizopods ’ and is therefore renamed Cercozoa" (TC-S 1998 BiolRev:203)

Of course, that was Tom's version of Rhizopoda to begin with. Taxonomy gets very fun when different people at different times mean different things by the same name. Can't seem to find the etymology of Cercozoa, but the formal description reads pretty much like 'miscellaneous eukaryotes with thin pseudopodia'. And that they are.

While Cercozoa was initially based loosely on morphology and sketchy data from the dawn of molecular phylogenetics, it mostly survived intact over the years, and grew further (with various things shaved off too, of course). The original members were Phytomyxids (incl. the plant pathogen Plasmodiophora), Reticulofilosa (basically, Chlorarachniophytes) and Monadofilosa (Cercomonas, Gymnophrys, Euglypha and Spongomonas are given as original examples). Curiously, all of them survived the onslaught of molecular reality (or so we hope...). Stuff has been added, like Ascetosporea (paramyxids and haplosporidia; added in TC-S 2002 IJSEM) and the gromiids, as well as various obscure incertae sedis orphans and a few refugees from 'Heliozoa'.

Eventually, the Cercozoa got 'sistered' to the forams (Keeling 2001 MBE) by ACTIN phylogenies, which got taxonomically recognised in the TC-S 2002 IJSEM revision of The Book of Tom by declaring the holy union of Retaria (forams and rads) and Cercozoa as Rhizaria. Going overboard as usual by adding in Heliozoa and Apusozoa, of course. We're talking about the mad taxonomist here ;-) (now someone needs to make that into a pop culture phenomenon to rival mad scientists..."And along comes the evil mad taxonomist...and RENAMES EVERYTHING!" *cue spooky music*) The group still lacks any solid synapomorphies (shared derived characters); the situation is such that even the use of obscure ultrastructural elements has been attempted, such as Cavalier-Smith's "transitional nonagonal fibre" (TC-S 2008 Protist) – even one of his own past students has no idea what he meant there!

And a whole bunch of other stuff happened but I think that was enough Historical Taxonomy (would make the most popular course evar, srsly) for...the month. Ok, so have we lost everyone yet? Or have the wiser ones employed the high art of The Scrollbar and skimmed accordingly? In any case, I'd like to very briefly and shallowly run over a few of the major cercozoans to give you a taste of the phylum, and just how diverse and varied it is. Things will be skipped, including, quite possibly, The Most Interesting Thing Ever Because You Studied it for the Past Ten Years. Apologies in advance. TMITEBYSiftPTY will get its chance, someday.

Some phylogeny and taxonomy sources: TC-S & Chao 2003; Bass & TC-S 2004; Bass et al. 2005; Pawlowski & Burki 2009; Chantangsi et al. 2010.

(L: Pawlowski & Burki 2009; R: Chantangsi et al. 2010)

To be continued in Part II – Endomyxa.

References
Bass D, & Cavalier-Smith T (2004). Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). International journal of systematic and evolutionary microbiology, 54 (Pt 6), 2393-404 PMID: 15545489

BASS, D. (2005). Polyubiquitin Insertions and the Phylogeny of Cercozoa and Rhizaria Protist, 156 (2), 149-161 DOI: 10.1016/j.protis.2005.03.001

CAVALIER-SMITH, T. (1998). A revised six-kingdom system of life Biological Reviews of the Cambridge Philosophical Society, 73 (3), 203-266 DOI: 10.1017/S0006323198005167

Cavalier-Smith T (2002). The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. International journal of systematic and evolutionary microbiology, 52 (Pt 2), 297-354 PMID: 11931142

Cavalier-Smith, T., & Chao, E. (2003). Phylogeny of Choanozoa, Apusozoa, and Other Protozoa and Early Eukaryote Megaevolution Journal of Molecular Evolution, 56 (5), 540-563 DOI: 10.1007/s00239-002-2424-z

CAVALIERSMITH, T., LEWIS, R., CHAO, E., OATES, B., & BASS, D. (2008). Morphology and Phylogeny of Sainouron acronematica sp. n. and the Ultrastructural Unity of Cercozoa Protist, 159 (4), 591-620 DOI: 10.1016/j.protis.2008.04.002

Chantangsi, C., Hoppenrath, M., & Leander, B. (2010). Evolutionary relationships among marine cercozoans as inferred from combined SSU and LSU rDNA sequences and polyubiquitin insertions Molecular Phylogenetics and Evolution, 57 (2), 518-527 DOI: 10.1016/j.ympev.2010.07.007

Keeling PJ (2001). Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home? Molecular biology and evolution, 18 (8), 1551-7 PMID: 11470846

Nikolaev, S. (2004). From the Cover: The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes Proceedings of the National Academy of Sciences, 101 (21), 8066-8071 DOI: 10.1073/pnas.0308602101

PAWLOWSKI, J., & BURKI, F. (2009). Untangling the Phylogeny of Amoeboid Protists Journal of Eukaryotic Microbiology, 56 (1), 16-25 DOI: 10.1111/j.1550-7408.2008.00379.x

Diagrams that make me cry, part LargeNumber

I was calmly blogging about real content, of course procrastinating simultaneously by writing pieces of stuff for work, as well as planning on possibly contemplating actually doing the readings for tomorrow's paleontology class. In the intro chapter titled "Fossils and Evolution", we get shown the following figure as The Taxonomic System, with a mention in passing the there have been some minor adjustments in the past, such as Three Domains, etc. Of course, such trivial taxonomic nitpicking is apparently of no use to paleontology students, so we'll use the horribly outdated Whittaker 1963 classification which should never be seen outside history of science lectures...

Aaaaaaaaaaah! Gotta love the 3:2 vertebrate:invert ratio too. Apparently bryophytes and 'pteridophytes' don't actually exist either. My own kingdom makes me weep. Also, for personal sanity, ignore the "Protoctista". That's just Margulis trying to feel special. And somehow succeeding outside her own field. (Levin 1999 Ancient Invertebrates and Their Living Relatives. Prentice Hall, NJ)

'Oh but the textbook's from 1999, cut 'em some slack with the volatile ever-changing taxonomy mess!' If they had used the Woese tree, which I have other personal issues with, I'd be fine with it. Of course, Woese tree in 2010 is a bit irritating, but I can still live with that. But...what truly adds insult to the injury, and rubs various salts even deeper into the bleeding wounds of my inner soul – THAT FUCKING PIE CHART!

"Proportions of members of each kingdom living today"

Hang on, gonna go break some furniture with energetic *headdesk* maneuvers. And my forehead with epic *facepalming*. BRB.

...ok, back. Lab benches are quite sturdy, it turns out. I'll just let Star Trek and internet memes take care of this:

Source: The Internets. All of them.

And they teach this as an uncontroversial, neutral fact. When, in fact, reality looks more like this:

Proportions of total marine biomass and abundance occupied by the only noticeable taxonomic groupings. Also, anyone who replaces "eukaryotes" with "protists" must be pretty freaking awesome. And/or actually understand biodiversity. (Suttle 2007 Nature Rev Microbiol)

I don't mean to bash the textbook itself. Aside from the little taxonomical issue there, the rest of the book seems quite interesting and perhaps a great source for paleontology (not being of that field, I have little idea). It just bothers me when something so cheap and simple to fix is left ignored and perpetrated on and on as students fail to learn any better, and teach what the learned, and further students learn that, and so on, ad infinitum, until we're left wondering why modern anthropology graduates seem to think evolutionary biology progressed little since Darwin's time. It's kind of annoying. And detrimental to efficient progress in all relevant fields. Not even asking for a new section in the book; just fix what's already there!


Ok, my blogging spirit is back now. Time to write up actual posts, relying on the creative writing juices (if any) unlocked by the power of RANT.

Taxonomic tidbit: parabasalids and strippers

Sometimes the taxonomist's character lies concealed in the etymology of a new taxon name:

"The arrangement of the long cilia, clothing the body, reminded him of the nymphs in a recent spectacular drama, in which they appeared with their nakedness barely concealed by long cords suspended from the shoulders, and this arrangement has suggested the name applied to the parasite." Leidy 1877 Proc Acad Nat Sci Philadelphia (h/t PJK)

So yes, Trichonympha (third from left in the blog header), reminded some proper Victorian scientist of his latest stripper experience. And this is why it sometimes pays to read the original taxonomic descriptions.

Also, apparently it wasn't too weird for the author to refer to himself in third person back then...

Assorted musings on barcoding

Speaking of Guelph (see prev post), Paul Hebert, the Canadian barcode god (or so I'm told), gave a talk today about...well, barcoding life. Overall, it was a good talk, and I can see why he's in charge of a bunch of stuff -- his talks are quite convincing. At least he's convinced me not to automatically fear/resent barcoding. Not that anyone asked for my opinion on these matters, but this is my little corner of the internet so I'll ramble some thoughts about it. (yes, ramble. You've been warned.)

I have a few traditional taxonomist friends who have painted a pretty negative image of it for me; there's even a mycology grad student who does quite a bit of barcoding herself and has come to be quite skeptical of it. Furthermore, being fascinating by the biology of things rather than their mere existence, all those billions of species don't exist as far as I'm concerned until they've been actually studied. And no, 600bp of a conserved gene sequence does not qualify.

The value of being able to identify something in the field without having to look at the 'length of the spine on the 3rd tarsus', to [badly] paraphrase Hebert, is clearly there. His dream of a handheld barcoding device perhaps could be especially useful to people who actually do fieldwork (wait, there's biology outside the lab? WTF?), although how you can 'read' a DNA sequence sufficiently quickly still eludes me. Don't you still have to wait for crap to get amplified? Would be awesome if they have some way of doing really quick (and cheap) PCR, that could come in quite handy even for the model organism crowd. I don't necessarily enjoy waiting 2h to genotype some crap (oh, and another hour before that to extract gDNA). But I digress. This barcoding technology stuff does sound awesome.

However, I often have some skepticism towards awesome-sounding revolutionary technology -- too often people get carried away in the hype, and start attempting to use machinery to replace human intellect. That can be dangerous. Some tasks appear more mechanical than they really are, and it seems taxonomic identification and description is definitely among them. Most reasonable barcoding proponents don't seem to dismiss traditional taxonomy, but there is the fear that public opinion and funding agencies might not feel the same way. And as much as we love to reduce everything within our reach to digitised strings of characters, we still have to interact with the physical world.

Hopefully, the barcoding 'revolution' (that word is automatically associated with TC-S for me now, for some reason...) would be used in combination with the insight, knowledge and intelligence (ie talent) of traditional taxonomists, rather than attempting to replace them. Molecular phylogeny is substantially more reliable than anything morphology-based, as anyone who's wandered around in the protist kingdom would know*. But that doesn't mean morphological evolution is now to be ignored - on the contrary, molecular biology has made it much more exciting now that you could see how the organisms are related, and then investigate their morphology.

Another thing that annoys me is this whole 'species counting' business. You know, when someone spits out "There are 10 000 species of blah in blah", and the media picks up on it and we end up with "OMG, there are 20 000[sic] species of blah in [incorrect] blah!!!one! We are doomed/saved/awesome/cured of cancer[pick one]!" Seriously, who cares? Does it really matter whether there's 10 000 reproductively isolated clusters of something or 15 000 or 100 of them? Does counting them reveal anything profound? The majority of life on earth doesn't particularly care much about reproductive isolation! And among the few sorry exceptions where reproductive isolation becomes somewhat important (metazoa mostly; plants turn out to be a little more promiscuous), all species-counting can say is perhaps something interesting about...evolutionary dynamics of reproductive isolation. Furthermore, this ignores intraspecific variation, which is important and seemingly ignored by many evolutionary ecologists. And then we wonder why people get confused about where variation are. They see diversity as being composed of heavily discrete units, which may perhaps be confusing when trying to understand evolution itself.

That's not to say variation isn't important - it is, and it's definitely fascinating. But it does not do it much justice to simplify everything down to 'species', which then become treated as solid units of variation, rather than a subset thereof. It's far more complex than a mere absense of interbreeding.

Barcoding may be quite interesting for exploring how asexual vs. sexual (and facultatively sexual) organisms tend to cluster, how this clustering differs among various phyla, habitats, etc. Hebert did mention plans to pursue some of those directions, and it will be interesting to see what turns up.

Lastly, they seem to be using a single gene for barcoding. I think that's might even be what 'barcoding' would mean, strictly speaking. This is worrisome. Single gene phylogenies are CREEPY and SCARY o_O. I wouldn't touch one with a 10 foot pole anymore. Of course they picked something that [they think] is extremely conserved and constant (yet flexible enough to allow for variation at their desired resolution) - a commonly-shared mitochondrial gene (by the sound of it, Cox1 perhaps). They say it's conserved and reliable. Awesome - that's what they said about SSU rDNA. How did that turn out?

Bits of freaking FUNGI ended up as basal to all Eukaryotes, along with diplomonads, parabasalia and archamoebae, which have little to do with each other. Oh, and they still print this tree (which was quite a breakthrough at the time, to be fair; but things have changed in the last couple of decades...) Why? Some lineages experience faster rates of evolution than others, and this leads to much greater sequence divergence from its neighbours, which often screws things up in the alignment algorithms, resulting in Long Branch Attraction - things that diverged a shitload relative to everything else tend to cluster together. Some normally stable genes under certain circumstances can go haywire. Single gene trees a fucking dangerous. So are multigene trees, but we haven't got much else going for us...

Basically, the problems that plague SSU alignments can also fuck with barcoding. Especially once you wander outside the small comfy familiar home we call Metazoa...

Of course, everyone knows that, but I wouldn't be surprised if people suddenly started worshipping (and publishing) single gene trees based on barcode sequences. Faith in the scientific community seems to be inversely proportional to experience with it...

So yeah, it's exciting, but we must also be cautious. I guess that would be my [rather unhelpful] answer to pretty much everything...

Do you guys have any thoughts?

*Morphological classification led to almost all non-photosynthetic basal stramenopiles/heterokonts being mistaken for something considerably different: Labyrinthulids, oomycetes and Blastocystis were considered to be fungi, opalinids were 'ciliates', actinophryids were 'heliozoa', and there's even a genus called Pseudobodo (a bicosoecid) that was mistaken for...bodonids! Molecular phylogeny continues to churn out one surprise after another!

'Crhaptophytes' and the Chromalveolate Hypothesis

Procrastination with about a million things (including overdue blog posts) is the perfect time to blog a freshly published paper. Although I can't quite figure out how to make the preceding sentence make any sense syntactically...

Warning: This post contains copious amounts of obscure phylogeny and taxonomy. Discussed by a cell biologist. Proceed with caution.

I've probably carelessly alluded before to the Chromalveolate Hypothesis by Cavalier-Smith (eg. 2002 Curr Biol). In any case, I tend to go by the assumption it may be correct, since I'm a cell biologist and therefore required by federal law not to care about evolution. There's powerful/annoying(depending which side you're on) evidence pointing both ways, so the thing is a bit of a mess. I know, mess in protistological taxonomy? No fucking way!

Let's zoom in to one of Tom Cavalier-Smith's many warzones:

(based on Keeling et al 2005 Trends Ecol Evol; bonus marks for recycling diagrams from past talks, ignore box)

The green dots indicate the presence of photosynthesis in respective lineages. This is just to get an idea of where these things are - members of Chromalveolata include ciliates, dinoflagellates, apicomplexans (eg. Plasmodium, responsible for malaria), diatoms, kelps, oomycetes (eg. Phytophthora, the other organism behind the Irish famine, besides H.sapiens and their sadistic and incompetent governance.) and the possibly less familiar Haptophytes (chalk in cliffs of Dover).

Now that seems like a rather diverse mix of stuff to have in one kingdom, and it is. You have multiple independent instances of multicellularity, lifestyles from parasitism to phagotrophy to photosynthesis to osmotrophy (think fungi) to mixotrophy (eg. photosynthetic predators) and beyond. It's rather hard to believe that the entire grouping may be held together by... a single red algal plastid endosymbiosis event. (TC-S 2002) And some don't. In fact, the evidence is rather strong both for and against what is called the Chromalveolate Hypothesis: where 'chromists' (stramenopiles + cryptophytes and haptophytes) and alveolates share a single secondary endosymbiosis event.

If the Chromalv. hypothesis is accurate, you would expect many lineages to be photosynthetic or contain relic plastids. Furthermore, you'd expect lineages devoid of plastids to at least contain some relic plastid-derived genes in their genome. Those characters should also point towards a single origin, as opposed to two or more independent endosymbiosis events (eg. from different red algae).

I've prepared an overview of what the Chromalv. hypothesis 'looks like', hopefully not plagued by too many inaccuracies:

(This almost looks like a TC-S diagram. I guess that's just inevitable. Red - groups containing photosynthetic lineages with a red-algal derived plastid; Green - group with green algal secondarily derived plastid. EDIT: And that's KAtablepharids, not Ketablepharids...EDIT#2: Forgot the excavates - place them somewhere between the archaeplastid-chromalv node and the root...)

Going clade by clade, some evidence that supports single chromalv. plastid origin is:
- Apicomplexa, a vast group of intracellular parasites such as not-so-friendly(to us) critters like Plasmodium and Toxoplasma, have been found to posess reduced plastids, called apicoplasts (eg. reviewed in Waller & McFadden 2005 Curr Issues Mol Biol). Malaria turns out to be an algal disease. There's plenty of other examples of algae-turned-parasites, but we've got a TC-S hypothesis to cover...
- Basal to Apicomplexa is a photosynthetic alga called Chromera, with a red-algal-derived plastid, which further supports an algal origin of 'Apies'. (Moore, Oborník, Janouškovec et al. 2008 Nature)
- Dinoflagellates, Ochrophytes (group containing kelps and diatoms), Cryptomonads and Haptophytes all have photosynthetic members with a certain red-algal derived plastid. Now, the fuss is about whether they all got their plastids once, with the plastid-less lineages having lost them through time, or multiple times within the Chromalveolate kingdom.
- (more evidence is discussed in Keeling 2009 JEM)

Refer to the diagram below. Endosymbiosis is accepted by everyone but Marguilis to be a very unlikely event, and therefore very unparsimonious to postulate for every photosynthetic lineage you see. You would expect some lineages to lose their photosynthetic ability, and even their plastids altogether. However, since endosymbiosis usually results in gene transfer to the host, you should be able to find plastid-derived genes in most lineages. This means that both plastid-bearing and plastid-less lineages should be distributed fairly haphazardly, without too much non-photosynthetic stuff clumping around basally. Unfortunately, that is annoyingly not the case entirely:

Prior to the discovery of Chromera and apicoplasts, the Chromalv. hypothesis was rather weak in Alveolata, with ciliates and apies both being non-photosynthetic. Furthermore, the basal lineages of Stramenopiles are also non-photosynthetic, with things like 'fungal' oomycetes, labyrinthulids, opalinids ('ciliated'-looking frog gut endosymbionts), and parasites and gut commensals like Blastocystis and Proteromonas that seldom see the light of day. Among the Crypto-Hapto clade, it also seemed like the non-photosynthetic stuff like Katablepharids and Telonemids were basal to a monophyletic crypto-hapto grouping. When there's a long stretch of basal lineages devoid of a certain trait, it becomes more unlikely for that trait to have been acquired early on. Compare the bottom two trees - which topology is more likely to agree with an ancient common plastid origin?

It is fairly certain that the alveolate clade shares a common endosymbiotic event - there are even some seemingly-algal derived genes in ciliates, although that remains to be confirmed (Prieto et al. 2008 Curr Biol). Among the Stramenopiles, things seem to be clearing up a bit - some Oomycetes seem to have putative plastid-derived genes, for example. And something nice was recently found in the Cryptomonad-Haptophyte group.

Cryptomonads and haptophytes are the more familiar members (well, relatively) of the newly established Hacrobia, or 'Crhaptophytes'. Cryptomonads are fairly ubiquitous little algae with a characteristic gullet lined with ejectosomes - organelles that basically sting their prey. Cryptomonads are special in that they have nucleomorphs - highly reduced nuclei left behind from the red algal secondary endosymbiosis. The crypto plastids actually have a remnant red algal nucleus in the remainder of the endosymbionts cytoplasm. Nucleomorphs are known in one other organism - chlorarachniophytes, which have a green algal secondary endosymbiont (see the big chromalveolata diagram above). Due to the size constraints and reduced need for making own proteins (since the host can provide them), the nucleomorph genomes have some rather interesting features, which should be covered at a later date.

Haptophytes are generally spherical things, characterised by having a protrustion (haptonema) between its flagella, which it may use to catch prey. The more famous haptos are covered in little scales (coccoliths), and are great contributors to sedimentation, often resulting in...chalk! Coccolith-bearing haptos are extremely tiny organisms, which can be seen from space. A taxonomic mess resulted from there being seemingly two types of haptos: heterococcoliths and holococcoliths. They were long considered asexual until Geisen et al. 2002 reported a half-hetero- half homococcolith-bearing haptophyte, which led to the discovery of a sexual lifecycle involving a diploid heterococcolith and a haploid homococcolith stage, illustrated here. It's very interesting how traditionally 'asexual' lineages seem to be foung otherwise, one by one...

(Source: Micro*scope (crypto); http://www.geo.uni-bremen.de/cocco/(hapto))

You may be wondering where the 'crhaptophytes' come from. Time for a piece of lab folklore told to me by a postdoc:

Once upon a time, when the support for the Cryptophyte-Haptophyte clade grew to near certainty, one of the authors of that paper coined the term 'Crhaptophytes', because it's a rather apt description of the grouping, and sounds pretty awesome. And they are tiny hyperactive pieces of crap. Apparently 'Crhaptophyte' didn't fly well with the ICZN/ICBN taxonazis, since their true intention is to make biological nomenclature living hell to deal with, and impossible to stay awake through. In short, a sleeping hell. So they had to come up with another name, and Hacrobia (ewww) it was.

Of course, postdocs may not be the most reliable people on the planet when it comes to storytelling to potentially gullible undergrads, and academic gossip in general is very oddly like any other kind of gossip. However, given the cast of characters involved, it's not altogether impossible.

Since I really prefer the term Crhaptophyte, I'll encourage its use wherever possible. You know, taxonomy should be fun! Wow, 'taxonomy' and 'fun' in the same sentence, without a negation.What has the world come to...!

Anyway, back to our story: Lets meet Roombia, named after a...robotic vacuum cleaner! (Okamoto et al. 2009 PLoS ONE)

(Okamoto et al. 2009 PLoS ONE - Roombia truncata; scalebar - 5um)

Sometimes a new organism is found that straightens out and stabilises messy trees (or utterly wrecks well-accepted ones...) The monophyly of our 'Chraptophytes' wasn't completely established until fairly recently, and the relationships of the organisms within that group were also murky. Sometimes the sequences just don't like you and spew out trees that make no sense. (Or so I'm told anyway - I actually work on 'real' biology, not just truncated versions of the Latin alphabet... =P) Roombia, along with some other data, has cleared up some relationships within the newly published taxon Hacrobia.

If you go back up to this diagram, the relevance of this finding to the Chromalv. hypothesis is evident in the bottom two trees: the placement of some non-photosynthetic lineages among both of two distinct clades - one with haptos and one with cryptos - takes care of one more troublesome clade with long stretches of basal non-photosynthetic crap chomping away at the likelihood of a single origin. However, there's still the issue of whether Hacrobia is sister to Stramenopiles + Alveolates (good for Chromalv.) or Archaeplastids (bad); as well as establishing whether the "stramalveolate" (can we call it that for now?) plastids and Hacrobia plastids are likely to share a common origin between them.

So it looks like the chromalveolate hypothesis is doing a little bit better, now that not all the basal lineages are non-photosynthetic; multiple plastid loss seems more plausible. However, if you look at one of the broader trees in the paper, it seems to show a pretty well-supported (bootstrap of 0.98) branching of Crhaptos with Archaeplastida. That would be very bad (eg. . However, this is only one gene, Hsp90, and the paper doesn't really discuss that anywhere. Furthermore, my sources inform me that the root(Archaeplastids, Crhapto, (Rhiz, Stramenopiles, Alveolates)) branching seems more likely at the moment. In fact, the little barely-noticeable hyphens under the branchings mean that less that half of the trees support that topology, so ignore everything I just said about archaeplastids and crhaptos. This is to remind us that you can't infer anything from looking at a single tree - biological data is inherently messy, no matter how pretty and crisp and clean the diagram...

By the way, this is by far not all there is to work around the Chromalveolate Hypothesis. There's so much more data pointing in both directions, but I have neither the time nor the qualification to write about it all... and hopefully I haven't butchered too much stuff in this post.

I guess the main thing to take home from all this is how messy and complicated the task of establishing relationships between organisms can be. One must be very skeptical of any models based on single evidence, such as single gene trees or morphology. Or even multiple gene trees, if other data is ignored. Weird shit happens in evolution, and some mysterious event in the past can seriously screw up our perception of the present. As can yet-to-be-discovered characters and phenomena: the Archaezoa were doing quite well until most of the 'amitochondriate' lineages were found to actually contain relics of mitochondrial presence. New data can completely turn trees upside down, roots left dangling all over the place. New data can also strengthen a model. You just never really know, and have to rely on logic, likelihoods and, admittedly, a fair amount of hunches. One must be flexible in the face of new evidence, yet skeptical of the interpretations and validity thereof. Such is life in the fragile wedlock of skepticism and wonder that is science.

PS: Image searches can lead to strange places. Like CreationWiki. Owww. I can feel parts of my brain rotting away and draining out of various cranial orifices:

"All haptophytes are asexual" WRONG. And WHAT THE FLYING FUCK does Blastocystis have to do with Apicomplexa?! Oh right, we reject evolution, therefore phylogeny no longer matters, you polyphylophilic* ignorant morons. Note the absense of references: everything seems to be stolen from Wikipedia et al. Shocking. AND OH MY FSM: "Baraminology"! o_O I'll just leave it at that...

*Adj. Having a fetish for knowingly using polyphyletic lineages. A known side effect of phylogenetic ignorance. Actually, I feel kinda bad bullying the 'epistemologically challenged'. It's more fun to pick on bad PNAS papers instead...
PPS: I'm a nerd: [after subscribing to Trends Ecol Evol feed via Reader]"I've singlehandedly just raised TrEE's IF by a good 10 points! "
My friend (hi!=D) is just evil: "send there a paper to pull it back."
[followed by more impact factor jokes...]

EDIT: David and Jan, thanks for the corrections!

Cavalier-Smith, T. (2002). Chloroplast Evolution: Secondary Symbiogenesis and Multiple Losses Current Biology, 12 (2) DOI: 10.1016/S0960-9822(01)00675-3

KEELING, P., BURGER, G., DURNFORD, D., LANG, B., LEE, R., PEARLMAN, R., ROGER, A., & GRAY, M. (2005). The tree of eukaryotes Trends in Ecology & Evolution, 20 (12), 670-676 DOI: 10.1016/j.tree.2005.09.005

KEELING, P. (2009). Chromalveolates and the Evolution of Plastids by Secondary Endosymbiosis Journal of Eukaryotic Microbiology, 56 (1), 1-8 DOI: 10.1111/j.1550-7408.2008.00371.x

Moore, R., Oborník, M., Janouškovec, J., Chrudimský, T., Vancová, M., Green, D., Wright, S., Davies, N., Bolch, C., Heimann, K., Šlapeta, J., Hoegh-Guldberg, O., Logsdon, J., & Carter, D. (2008). A photosynthetic alveolate closely related to apicomplexan parasites Nature, 451 (7181), 959-963 DOI: 10.1038/nature06635

Okamoto, N., Chantangsi, C., Horák, A., Leander, B., & Keeling, P. (2009). Molecular Phylogeny and Description of the Novel Katablepharid Roombia truncata gen. et sp. nov., and Establishment of the Hacrobia Taxon nov PLoS ONE, 4 (9) DOI: 10.1371/journal.pone.0007080

REYESPRIETO, A., MOUSTAFA, A., & BHATTACHARYA, D. (2008). Multiple Genes of Apparent Algal Origin Suggest Ciliates May Once Have Been Photosynthetic Current Biology, 18 (13), 956-962 DOI: 10.1016/j.cub.2008.05.042

Naughty nomenclature + Deconvolve This!

Taxonomy can actually be fun sometimes:

Tubifex longipenis

heehee... somehow there's this public image of academics being all mature and serious. In reality, those are rather hard to find...


Recent disappearance was due to leeching off a 2wk 3D live cell microscopy course that happens at UBC every year; they were nice enough to let local students attend lectures... and even leech off the food a bit... Great course, highly recommended for those who think microscopy is just putting shit on a slide and looking at it. Microscopy is a high art and a rather sophisticated science. Course is likewise quite recommended for those who realise that already...they have pretty toys cutting edge microscopes to play with test out for your research purposes.

So yeah, practice safe microscopy -- always use deconvolution on 3D data*! ^.^

Also, physics (and even chemistry) becomes surprisingly interesting when presented by the right people in the right context! Or maybe I'm just crazy... (but so are the course faculty and many students so no one noticed...)

*There is a debate on whether deconvolution works at all on plant material, which is rudely autofluorescent and absurdly packed with spherical aberrations sufficient to utterly destroy your PSF into a disturbing calculation-intensive mess. Our stuff is apparently notoriously shitty for decent microscopy, especially in confocal and multi-photon. And guard cells are among the worst in plants... so decon may not work there (Sorry, Prof. Pawley! >_> )