5min left for CoE submissions!

First off, you have 5min left to submit your post to the Carnival of Evolution. By the time you read this, chances are the submission deadline has passed.

I'll hopefully have the post done tomorrow night (Pacific Time)

Also, came across a funny quote:

"Scientists who fail calculus become biologists and those who flunk arithmetic become taxonomists." [source]

SO TRUE! I mean, uhhh... someone is going to kill me now...

Read more at How Many Species are there on the Planet? A final, definitive and precise answer.

Sunday Protist -- Auranticordis: "Orange Heart"

(Also the answer to MM12, which nobody got, although I haven't particularly followed up on the hints either...)

If you're ever low on ideas for your next taxonomic adventure, Cercozoa is one endlessly fascinating clade that never fails to offer surpises. In fact, the more you explore them, the less familiar they become. Cercozoa (TC-S 1998) can offer pretty much anything -- from photosynthetic amoebae to the utterly bizarre Phaeodaria to beautiful testate Euglyphids (including a case of separate primary plastid endosymbiosis!) to a wide variety of random semi-amoeboid-semi-flagellate things that glide about on their flagella and make faces at anyone trying to classify these things by morphology. Cercozoa are a mess, but a beautiful mess.

SEM from looking down at the anterior apex of the cell. Bar = 10um; Chantangsi et al. 2008 BMC Microbiol (open access)

The baby Nautilus looking thing that was so mischievously confusing is Auranticordis quadriverbis, a rare benthic tetraflagellate of a distinctive orange colour.

A - L: lobe, arrows: orange muciferous bodies; C - arrowheads: putative endosymbionts. D - arrowhead points to ventral groove. E - phase contrast showing flagella protruding from the ventral groove. Bar = 10um. (Chantangsi et al. 2008 BMC Microbiol)

The orange colour is caused by the muciferous bodies lining the ridges along the cortex. These bodies secrete mucilage upon disturbance, and may participate in adhesion to the surface. The membranous ridges on the surface are supported by bundles of microtubules, in the absense of any cell wall. An SEM of the ridges reveals the mucilage being secreted by the pores that line them:

Sem close-up of the ridges with mucilage. Scalebars: C - 1um, D,E - 0.5um
(Chantangsi et al. 2008 BMC Microbiol)

Curiously enough, Auranticordis posesses potential endosymbionts -- thylakoid-bearing orange bodies inside the cytoplasm. While those could be food particles being digested, the lack of different extents of digestion and their intact appearance suggests these endosymbionts may be long-term (as in kleptoplasty) or permanent (endosymbiosis). The similarity of the ultrastructure to free-living cyanobacteria actually suggests this may be yet another case of primary endosymbiosis, as in Paulinella! (cyanobacteria don't have to be blue-green, by the way)

TEM of putative endosymbionts. The lines at the edges are thylakoids, surrounding a prominent invagination of the inner membrane. Bar = 2um (Chantangsi et al. 2008 BMC Microbiol)

Inside the endosymbionts one can find viruses that look similar to the ones that infect free-living cyanobacteria. The idea of a virus attacking your organelles, while not actually surprising, is still kind of cool!

Higher magnification TEM of the putative endosymbiont. B shows detail of the thylakoids C - cleavage furrow (arrowheads) supporting the idea of this body being an endosymbiont rather than a food particle, SC - sac-like vesicles. D - Viral particles at the thylakoid-free core. E - detail of the prominent inner membrane invagination. G - close up of more viral particles, (bar=0.5um) with an inset showing a complete one (bar=0.2um) (Chantangsi et al. 2008 BMC Microbiol)

Unfortunately these organisms are rare, so it's difficult to establish whether these pigmented bodies are in fact a third known case of primary plastid endosymbiosis. Wouldn't be so shocking after Paulinella, but still kind of cool. Perhaps primary endosymbiosis isn't as rare as previously thought, and that, were it true, could have a profound impact on our understanding of eukaryotic evolution. Conventionally, plastid gain is used as a very unlikely feature, and weighed heavily in analyses of parsimony. But the real picture could actually be much messier.

I hope you've enjoyed this brief encounter with an enigmatic, obscure Cercozoan. Warning: There's more where that came from, so expect more Cercozoa in the future. I really love that group...

Reference:
Chantangsi, C., Esson, H., & Leander, B. (2008). Morphology and molecular phylogeny of a marine interstitial tetraflagellate with putative endosymbionts: Auranticordis quadriverberis n. gen. et sp. (Cercozoa) BMC Microbiology, 8 (1) DOI: 10.1186/1471-2180-8-123

Our very own Tree of Eukaryotes

Time to unveil what I've been up to for the past several Friday nights. I figured that after nearly a year and a half, and almost 20K page views, it's time for our blog to grow up a bit. What we need is our very own tree.

Remember how I often refer to the Keeling et al 2005 tree when pointing out where some obscure organism lies on the 'map'? Well, that tree is 5 years out of date now. In fields like molecular biology and genomics, a lot can change in five years; compounded with how the protistan phylogeny was still in murky, squishy swamp of a mess only about 10-15 years ago, the current tree is far from static. But five years is a little too old for now, don't we think? Especially after there's been some massive 'kingdom'-level rearrangements lately, like Rhizaria being shoved amidst the Chromalveolates, and Cryptophytes+Haptophytes+Centrohelids forming a sizeable clade of their own -- Hacrobia. Protist phylogeny and taxonomy is rather volatile.

But there's another reason I decided to go ahead and make my own tree. Outdatedness will eventually haunt pretty much any hypothesis or model ever made, so that's not too much of a worry. But I really really wanted my very own tree, in vector format, that I can fiddle with and modify at whim to illustrate my point, or map characters onto it, or rearrange stuff, add taxa, etc. You can't really do that with someone else's tree, especially since you seldom have the original. After all, while I still have limited experience and lack qualifications, I do have access to volumes upon volumes of protistology literature, and even more importantly, some rather prominent members of the field. Thus, armed with PowerPoint, insanity and reduced sleep, I've ended up with a monster of a tree. And while it's nowhere near finished, and probably never will be (since science itself escapes ever being 'finished'), here is the first installment:

A tree of eukaryotes, v1.0. Not a real phylogeny (that is, no sequences were harmed aligned in the making of this diagram), just my own interpretation of the various sources listed at the bottom -- subject to error, and change. Please don't take this tree too seriously! (or any other tree, for that matter...) Feel free to use, modify and distribute, as long as the attributions are left intact =D
A Tree of Eukaryotes by Psi Wavefunction is licensed under a Creative Commons Attribution-Non-Commercial-Share Alike 2.5 Canada License.
CORRECTIONS (to come in V1.1):
1)Branching order of kinetoplastids + diplonemids messed up when moving things around; supposed to be: (diplonemids,(bodonids,trypanosomatids))
2) Oxymonad phylogeny mostly unresolved, must collapse clade (thanks, Opisthokont!)
3)Extra copy of Gonyaulocoids floating around outside the tree -- will remove
4) unsquish some taxa...if possible

If you see anything definitively wrong, please let me know. As for the particularly murky groups, I had to go by some hypothesis, so some branchings are actually quite contested. Some messy spots were lazily sketched out as giant polytomies (eg. Cercozoa). The number of taxa per clade is not in any way meant to represent its actual diversity, which I consider to be fundamentally arbitrary and pointless unless you have all the species, and have the same standard of 'species' across all groups. Good luck with that. The representative taxa were picked rather arbitrarily, and the width of the clades is largely influenced by my own tastes.

Ok, enough with the disclaimers -- just enjoy!

One very interesting group, the incertae sedis, were unfortunately left out -- for they do not have a home. While we go about our daily lives content with knowing our place in the tree (or so we think anyway), these poor creatures are left alone in the cold, unloved and unclassified. I think we should all take a moment to reflect upon their plight, and perhaps spare some change and help find at least some of them a home...look how cute and fluffy they are!

I was going to someday add pictures to go along with at least the more prominent taxa -- would that be helpful?

Not gonna cite all 33 sources with ResearchBlogging, but here's some of the major ones:

CAVALIERSMITH, T. (2003). Phylogeny and Classification of Phylum Cercozoa (Protozoa) Protist, 154 (3-4), 341-358 DOI: 10.1078/143446103322454112

Cavalier-Smith, T., & Chao, E. (2006). Phylogeny and Megasystematics of Phagotrophic Heterokonts (Kingdom Chromista) Journal of Molecular Evolution, 62 (4), 388-420 DOI: 10.1007/s00239-004-0353-8

James, T., Kauff, F., Schoch, C., Matheny, P., Hofstetter, V., Cox, C., Celio, G., Gueidan, C., Fraker, E., Miadlikowska, J., Lumbsch, H., Rauhut, A., Reeb, V., Arnold, A., Amtoft, A., Stajich, J., Hosaka, K., Sung, G., Johnson, D., O’Rourke, B., Crockett, M., Binder, M., Curtis, J., Slot, J., Wang, Z., Wilson, A., Schüßler, A., Longcore, J., O’Donnell, K., Mozley-Standridge, S., Porter, D., Letcher, P., Powell, M., Taylor, J., White, M., Griffith, G., Davies, D., Humber, R., Morton, J., Sugiyama, J., Rossman, A., Rogers, J., Pfister, D., Hewitt, D., Hansen, K., Hambleton, S., Shoemaker, R., Kohlmeyer, J., Volkmann-Kohlmeyer, B., Spotts, R., Serdani, M., Crous, P., Hughes, K., Matsuura, K., Langer, E., Langer, G., Untereiner, W., Lücking, R., Büdel, B., Geiser, D., Aptroot, A., Diederich, P., Schmitt, I., Schultz, M., Yahr, R., Hibbett, D., Lutzoni, F., McLaughlin, D., Spatafora, J., & Vilgalys, R. (2006). Reconstructing the early evolution of Fungi using a six-gene phylogeny Nature, 443 (7113), 818-822 DOI: 10.1038/nature05110

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

Lewis, L., & McCourt, R. (2004). Green algae and the origin of land plants American Journal of Botany, 91 (10), 1535-1556 DOI: 10.3732/ajb.91.10.1535

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

Taylor, F., Hoppenrath, M., & Saldarriaga, J. (2007). Dinoflagellate diversity and distribution Biodiversity and Conservation, 17 (2), 407-418 DOI: 10.1007/s10531-007-9258-3

And many more!

Awesome flash game: Microbe Combat

http://www.flashraiders.com/242-Microbe-Combat.html

All we need is to make it more realistic, add bacteria (I hope the author(s) realise bacteria don't phagocytose, proving those microbes to be eukaryotic...they do seem to have nuclei though), add a few more organisms like amoebae, flagellates, a Hypermastigote or three, and...PARASITES! =D and we have a whole new genre of gameplay!

This could be so pretty! And sexy, since we're talking about eukaryotes. Any programers out there? *drools*

Anyway, must go back to play some more get real work done.

ME TARZAN! Simple morphology: the result of a large, complex, multicultural language community?

For a brief change of topic, let's take a look at language evolution! I wrote up the following novel review paper blog post for a non-biological evolution seminar course I'm involved with. We're essentially first examining various key topics in evolutionary biology (alas too briefly!), exploring how the by-now well-established field of evolutionary linguistics successfully applies evolutionary theory to languages (technically much of it before biology came along...linguists invented phylogeny!), and then playing around in the vast and violent Wild West that is cultural evolution, hopefully sufficiently equipped by then to discriminate shit from gold and ward off the marauding bands of pseudoscientists.

For the record, I have a very limited linguistics training - only a handful of undergrad courses as my electives, so please point out and criticise any inaccuracies (and be generally skeptical, although I'd imagine most of my readers are by now =P) Any errors in attempts at explaining the linguistics behind the following paper are mine, and mine alone. Slightly edited to suit broader audience. Enjoy!

---

Have you ever wondered why English seems so simple compared to some other languages, particularly those notious for complex grammar like Russian or German? Have you wondered whether there was any reason why the local [Pacific Northwest] languages are so complex and filled with intricate grammar?

May I interest you in a very recent awesome paper from PLoS ONE:

Language Structure Is Partly Determined by Social Structure Lupyan & Dale 2010 (open access)

They examined 2236(!) languages and looked for correlation between their morphological complexity and the 'linguistic niche' -- whether the language is spoken over a vast area mostly by strangers, or used within a small tightly-knit community. The majority of the world's languages are 'esoteric' (smaller population, fewer neighbouring languages, smaller area; eg. Tatar, Piraha, Ju|'hoan, Nuu-chah-nulth), contrary to what is most obvious to us, ie the 'exoteric' languages like English or Swahili. One would expect that the use of an exoteric language as a lingua franca may result in some changes in its structure, as its 'purpose' or 'function', if you will, is quite different. Anyway, they found that:

1. Exoteric languages tend to be isolating; that is syntactic stuff (tense, person, etc) is marked by independent morphemes rather than affixes or other inflections. For example, in Russian (which is still very exoteric, but less than English or Mandarin) house would be /dom/, but to say "of [the] house" (that is, house[gentitive]) you say /doma/, using a suffix instead of a preposition to indicate the case. In this case, English would be more of an isolating language, whereas Russian is more of a fusional one. By the way, we Russians do use a mixture of both suffixes and prepositions -- would be interesting to see if the use of prepositions intensified over time as Russian became more dominant in its region.

2. Exoteric languages tend to have fewer case markings (see Russian example above); furthermore, Exoteric languages seem to use the Nominative/Accusative system (English, Russian, German, etc) rather than the Ergative/Absolutive system (eg. Basque), which still completely eludes me. Probably because it's rare and unusual. As far as I can 'understand', ergative languages basically use the object as the subject of the verb. Ie, 'dog walked' would actually mean 'walked' acted on the dog, ie the 'dog was walked'. Now 'dog walked boy' would mean 'the dog was walked by the boy', so the primary argument of the verb is the object, not the subject. Or something like that.

When I was randomly reading up on some German back in the day, it was interesting to find their case system to be completely in ruins -- it was obviously about to become the grammatical analogue of a pseudogene! Many of their suffixes either repeat in different instances, or don't even exist anymore. It's a mess to learn, and it seems like modern German relies on their case system less and less. Furthermore, Old English had cases. Yes, this language once had a hard-core, well-structured and absolutely essential case system, just a few centuries ago! I wouldn't be surprised if German cases go the way of the English ones in a few hundred years... for the record, Proto-indoeuropean had something like 8 or 9 of them.

3. Exoteric languages have fewer grammatical categories marked in the verb -- some of you may remember from learning French (or Spanish, or German) the billions of different conjugation schemes you had to memorise for the verbs -- damn things had to agree in number, gender, various intricate tenses, aspects etc. English seems to be much simpler morphologically. And it is. This is how we inflect 'walk' in English: (remember I'm talking strictly about morphology -- the syntax is still quite complex and intricate)

I, we, you, they - walk; he, she, it - walks

past - walked

progressive - walking

Now to compare with Russian: infinitive -- /gulyat'/ (to go for a walk) (picking regular verbs)

[1st person singular] /gulyayu/ [2nd p sg] /gulyayesh/ [3rd p sg] /gulyayet/

[1st p plural] /gulyayem/ [2nd p pl] /gulyayete/ [3rd p pl] /gulyayut/

past: [masculine signular] /gulyal/ [fem sg] /gulyala/ [neuter sg] /gulyalo/ [plural] /gulyali/

adverbial participle: /gulyaya/

imperative: [2sg] /gulyay/ [2pl] /gulyayte/

And probably a few more I missed. Now, Russian is a piece of cake compared to perhaps MOST of the world's languages!

4. Exoteric languages tend not to mark noun-verb agreement. As we've seen above, English is strikingly simple in that department -- there's only number agreement! Now, if French or Russian are intimidating, try thinking about inflecting the verb based on the subject AND the object AND how the verb is done by the subject onto the object... apparently, many languages do that. We had to look at Nuu-chah-nulth (aka "Nootka") in an introductory grammar&syntax course and oh my do they inflect for EVERYTHING. You have one word sentences that go on for a few rows of syllables...fascinating!

5. Exoteric languages seldom mark evidentiality by affixation -- that is, how a certain thing is known about is instead marked by verb choice and random modifiers. You may have noticed that academic writing requires a lot of cumbersome qualifiers and disclaimers embedded in every sentence, apparently. It tends to be that this may well be an inherent feature in research writing, or so I've heard. Some languages not only allow you to identify the nature of evidence for a statement, but actively require it much like English always requires tense (which, btw, not every language does; after all, 'today', 'in the past' and 'tomorrow' work perfectly fine instead!). It seems that this feature tends to mostly happen in the 'obscure' esoteric languages. Wikipedia has some nice examples from Pomo in the intro.

6. Exoteric languages are more likely to: a) encode negation lexically (eg. by EN 'no', FR 'ne...pas', RU 'nye', etc) rather than inflectionally (eg. JP -nai)

b) have obligatory plural markers (as in EN 'one cat - two cats', RU 'odin kot - dva kota'; in contrast, Japanese and Mandarin don't bother with obligatory plural markings, although in JP you could add -tachi ('many') if you really want (disclaimer: not a JP speaker...) This is why English with the stereotypical Chinese accent lacks plural marking: "Very cheap -- two dollar!" It is very curious that this is one of the very few increases in morphological complexity in exoteric languages.

c) less likely to have a distinct associative plural ("he and his friends", to use the example in the paper)

d) are more likely to have a dedicated question particle. English lacks this, but Japanese, for example, adds 'ka' at the end of an interrogative sentence. In a way, the particle is susbtantially simpler than all the weird obstruse syntactic movements you've got going on in English. Although I'd argue that simple tone raising is even more simple and likely ancestral too. Apparently tone raising is universally natural when you end a sentence with the expectation that someone else picks it up (which is what a question essentially is).

7. Exoteric languages a) are less likely to encode future morphologically. That is, English will not bother with a special inflection for future tense, will it? Even in French, where you have two forms of future tense, the lexical one is used more commonly in spoken form -- Je vais tomber as opposed to Je tomberai. There is a slight semantic difference, which is perhaps why both forms coexist, but less precise everyday use seems to be ok with the first form. Japanese famously "lacks" the future tense; however, as you can probably see by now, that is utter BS as English lacks it too! The difference is that French uses inflection, Russian uses a prefix with a strange aspect shift thing (that makes me pitty any students of the language...), English uses an auxiliary (will, going to) whereas Japanese uses simple lexical modifiers (eg. tomorrow, etc). Ashita watashi wa benkyou suru [tomorrow-I-[subj]-study-to do] is quite sufficient to express future tense!

Furthermore, exoteric languages are less likely to inflect for remote vs. proximal past tense (eg. happened recently vs. happened a looong time ago).

Again, I really want to stress that a lack of morphological marking for a grammatical category does NOT mean the language lacks a way to express it! English speakers are perfectly fine at distinguishing proximal past and remote past when they need to! ('Once upon a time' can be viewed as your classical 'remote past modifier')

b) more likely to mark imperatives with inflection, but less likely to distinguish singular vs. plural imperatives. English doesn't inflect imperatives, whereas Russian and French both do, although both seem to also mark singular vs. plural. Japanese, on the other hand, marks the imperative without inflecting for number (-(t)te-), so it wins the Exoteric Award for that category.

c) less likely to inflect posession. Eg. JP otoko no ken [man-of-sword] (that is, 'man's sword', Japanese uses postpositions rather than prepositions) but RU cheloveka mech [person.[gen]-sword] (more naturally, mech cheloveka, but to be parallel with the Japanese example). Japanese would be more exoteric in this case. English is weird so I won't go there. We really don't need to go into the DP Hypothesis today...

8. Exoteric languages don't seem to have definite vs. indefinite articles. (English fails this miserably - 'a' vs. 'the') If they do, they use separate words for them. Russian sort of lacks articles, although some argue it doesn't (syntax people are weird =P), so I can't tell what's going on there.

9. Less likely to use use demonstratives for distinctions. Ie. obligatory 'this here apple' vs. 'that there apple'. English doesn't do it, although you're more than welcome to if you'd like. Again, most of these points refer to obligatory grammar, rather than optional modifications you can add on. Inflections tend to be obligatory, and quite built in. By built in, I mean thoroughly engrained in your brain, usually outside your own awareness, if you're a native speaker -- I didn't realise Russian had cases (and SIX of them) until I was in my teens!

10. Exoteric languages tend to use lexical pronouns rather than expressing them morphologically (eg. as suffixes). Although in many languages where you do have subject-verb agreement, the pronoun becomes optional. Thus, this makes sense -- once you completely lose subject-verb agreement marking (as exoteric languages tend to), you are now required to have an obligatory subject pronoun. As in English. A wonderful example of an evolutionary ratchet!

SUMMARY: Languages spoken by more people in a wider area subject to more interlinguistic contact tend to be simpler morphologically than languages used in smaller isolated close-knit communities.

Now for some more of my own notes and ramblings:

First of all, let's point out that exoteric vs. esoteric is on a continuum; you may have noticed that English, which is blatantly exoteric, falls on the esoteric side for some characteristics, just like some Papuan languages would possess features of exoteric languages. It's not a binary distinction.

Regarding the degrading cases trend in Germanic (all IndoEuropean?) languages (see point #2): If cases degrade, how are they formed in the first place? The likelihood of a language simplifying should be higher than vice versa, yet we still find plenty of utterly complicated languages today. Why do they still exist? You can argue:

1. Many of those languages preserve ancestral features of some proto-proto-proto languages of the distant past, which were ridiculously complicated and later became honed down to something manageable in more-used languages. In other words, the complex languages evolved slower.

2. Under some circumstances, language evolution is actually driven towards complexity by whatever mechanisms (analogous to drift or constructive neutral evolution?). Incidentally, this circumstances seem to match those of esoteric languages -- small population size, etc.

I'll leave it as an optional exercise to the reader to devise experiments for testing those hypotheses (ie. I need to sleep soon...)

Onward to the bigger question: Why do the more widespread and promiscuous exoteric languages seem to have simpler morphology than the small and isolated esoteric ones? Isn't this a bit counterintuitive -- the so-called 'primitive' peoples should have simpler "ME TARZAN!" morphology while the refined Victorian Englishmen should sip their exotic teas to a conversation thoroughly inflected for evidentiality, twenty-something cases, five levels each of past and future compounded by five noun 'gender' categories and speckled with the fine Ergative-Absolutive alignment, preferrably with a touch of Nominative-Accusative just for kicks. Why is it that small, isolated linguistic communities, despite having arguably simpler social structure (in terms of numbers of components anyway), tend to have such amazingly intricate grammars and morphologies?

We can analyse this in three ways:

1. Simpler languages are more likely to be learned and thus spread easily. A complex language would find it harder to survive in a population of related simpler variants.

2. Languages with a larger and more diverse speaker population evolve faster, and thus become more efficient as speakers fail to grasp more complex grammatical elements, thereby 'mutating' the language, if you will. Bilingualism makes the matter worse as adult learners are notoriously bad at picking up new languages.

3. Simpler features are better at spreading themselves laterally*, thereby displacing more complex morphological characters through interlinguistic contact. Esoteric languages tend to be more isolated, and thus would remain safe from the viral simplicity**.

*(via areal linguistics -- characters like sounds or certain syntactic structures or inflections can be shared spatially between unrelated languages; a proposed classical example of this would be tones in East Asia -- the Mon-Khmer, Tai-Kadai and Sino-Tibetan languages are actually quite distantly related, despite appearing very similar to the western ear by tending to be tonal and isolating)

** There's actually a relevant field called 'linguistic epidemiology' which basically takes a similar approach. Would be interesting to see if anything's been said there regarding complexity.

Again, designing experiments and models are left as an exercise to the reader. Although my hunch is that all three may be involved to some extent, but perhaps the epidemiology argument may be most prominent, helped out by mutations and selection. Another fun topic to examine, perhaps?

This is actually quite reminiscent of Effective Population Size stuff in biol -- I have seen arguments that smaller populations can actually be less streamlined ('less adapted' than we'd expect them to be for their environment) than larger populations, where competition is much harsher and there is a strong pressure towards the efficient mean. I am now far outside of my fields though, and could be wrong in my interpretation; but it has been used as an argument (eg. by Michael Lynch, 2007 PNAS, if I understood correctly) as to why bacteria tend to be far more efficient and streamlined, with far less complex crap going on, than large multicellular eukaryotes, where some utterly ridiculous design ideas seem to be tolerated. This too would be fun to explore and/or model...

I'd like to conclude with the following proposition: 'Caveman language', Tarzan-style, was a widespread, multicultural language with hundreds of millions, if not billions, of speakers!

(And yes, I write these up for fun. Us research bloggers are a weird bunch. =P)

Reference:

Lupyan, G., & Dale, R. (2010). Language Structure Is Partly Determined by Social Structure PLoS ONE, 5 (1) DOI: 10.1371/journal.pone.0008559

Sunday Protist held hostage; MM feels neglected

Sunday Protist held hostage until some of you at least TRY to guess the current outstanding Mystery Micrograph*. Meanwhile, why don't you head over to the open random question and express your opinionated selves there? Come on, I thought everyone thinks about rooting eukaryotes in the back of their minds, right? *chirp chirp*

*Or until I finish the background reading for it anyway. I got myself into a bit of a taxonomic mess, and now that it's slowly crystalising (with structural defects, naturally) into something that makes sense. So now I can finally look up the relevant organisms and try to make a story. This is a totally foreign group for me...

Ok fine, I procrastinated: actually left campus today, had nice dinner, and now intend to crash to get up in time for my upcoming 8am class. I should really attend it more often, considering a) it's about metazoa, which I know nothing about; and b) I actually want to. No, seriously!

Carnival of Evolution #20 - Call for Submissions

The 20th monthly issue of Carnival of Evolution will be held hostage by the local protist denizens hosted here on Skeptic Wonder! =D

Calling for submissions of any evolution-related posts, either your own or someone else's. Some say that since it's no longer Darwin Year, evolution will drift out of the limelight and be forgotten by the blogging community. Let's prove 'em wrong!

Please use this form for submissions. Deadline: 18:00 PST (GMT-8:00) 31 January. Looking forward to reading them!

Random Question #02: So where do YOU think the root of Eukarya lies?

Things have been a bit quiet here lately. Let's start up a fight.

What are your views on the root of the Eukaryotic tree?
In the Unikonts, Bikonts, between them, don't recognise either as any valid group, etc?

Feel free to use abrasive language when defending your position. TC-S-like hyperbolic assertions are perfectly welcome to spice up the discussion.

If you're totally out of the loop (lucky bastard), how about this random more general argument: Holophyly or monophyly? =P
(I find this one always works when you wanna start up a lively discussion/raging war with some taxonomy/phylogeny friends...)
Also, see some musings in the comments for the previous post.

Yet another Woese Tree rant

o_O OMG, I'm getting infected by You-Know-Who's writing style...

I just sent this to my cell physiol prof:

The tree in slide 9 of the first lecture powerpoint is absolutely awful and grotesquely outdated (apparently based on Woese 1990). First of all, it is well-supported that the root is more likely to lie either between Eubacteria and Archaea+Eukarya, or within Eubacteria (I'm partial to the latter). It's rather murky in that particular diagram. Secondly, the eukaryote side of the tree makes one want to cry/punch a giant hole in the wall: Trichomonas and Giardia aren't exceptionaly likely to be the basal eukaryotes, and group reasonably well with Trypanosoma+Euglena, forming what may well be a monophyletic group. In any case, Trichomonas and Giardia seem to form a clade.

Dicty is WAAAY more closely related to Humans+Yeast than either Maize or Paramecium -- the later two are on a fundamentally different branch of eukaryotes -- the bikonts (eg. Cavalier-Smith 2009 J. Euk. Microbiol) or the corticates (Cavalier-Smith 2010 Biol. Lett.) Dicty, Humans and Yeast are members of a quite well-supported group (Unikonts), and this tree erroneously suggests that multicellularity evolved in the common ancestor of Plants, Animals and Fungi, which is completely wrong. Multicellularity evolved in each of those lineages independently, and in quite a few other lineages as well, up to ~16 times in the Eukaryotic kingdom (King 2004 Dev. Cell) and arguably a few times among prokaryotes as well (eg. Streptomyces).

I can't believe this is in a 2008 edition of the textbook! This tree has been outdated for at least a decade! How does one go about formally complaining with things like this? I refuse to let any suggestion of "crown/higher eukaryotes" vs. "stem/lower eukaryotes" go by unnoticed. The very notion of higher/lower organisms is thoroughly wrong and must be abandoned. Even in an introductory diagram. ESPECIALLY in an introductory diagram. Especially when they have the nerve to HIGHLIGHT Maize, Yeast and Humans as if they're some special enlightened life forms.

The era of Woese 1990 is over. We can move on anytime now...

The diagram comes from the "Big Alberts" text, 2008 edition. They should bloody know better by now! >.<

Candidate for the Twisted Tree of Life Award?

Also, their 'interesting' spelling of eukaryotes is in itself a rantworthy topic for some other day...

Phylomon, Protémon and "5 favourite organisms" meme

David Ng writes about the sad state of biodiversity/biology/nature education of kids when they obsess over fantasy instead, being unsatiated by what they know of the real world; this manifests itself in the form of Pokémon, etc. As a counter"attack", he suggests making Pokémon-esque Phylomon cards, perhaps eventually ending up with game-like rules and a way to reach out and educate children about the awesome diversity that exists far beyond the meagre attempts of human imagination. (ok, the hyperbolic assertions are my take). I think that would be awesome, especially if we could focus more on the world we cannot see so easily -- namely the microbes, aliens from a different scale.

A while ago my friend and I were discussing something similar, and 'Protémon' popped into my head. Yes, we could make a card collection/battle game starring various protists as characters. After all, since evolution has been around way longer than H.sapiens, its 'imaginative power' has expanded far beyond our own in that time. Of course 'intelligent design' via still-limited forsight can give an edge in creativity over non-human (ie non-cultural/linguistic) evolution, the damn thing's got about 3.0-3.5 billion years on us; there's still no way we could ever win!

Meanwhile, I randomly threw together this doodle in about 20min: fantasy anime videogame meet protistology. I swear no exogenous hallucinogenic chemicals were involved in this piece; the endogenous ones suffice, apparently...

Actually, in this particular screencap our protagonist is apparently ignoring the minor crap and charging straight at the boss: Cavalier-Smith 2006 Biol Direct (to the left of the drawing...)

I have class in 8h... Wish I had the speed-enhancing Stylonychia(-ish) protémon in real life to help me get to that class. Or a flying alarm clock shaped like Troglocorys. Damn I wish I were only ~100μm tall. On a second thought, maybe not...

And David Ng wants us to form a meme around his post:

"think of your five favourite organisms and why, suggest it for the Phylomon art community and pass it on?"

So consider yourselves tagged!

Ok, I'll do this one: (note, subject to change; I don't really have favourites, except for the first one)
1. Erythropsidinium (and other Warnowiid dinoflagellates) -- Unicellular dinoflagellate with a fucking IMAGE-FORMING CAMERA EYE. Need I say more?

2. Oxytricha (ciliate) -- Complicated bi-nucleate genome system, scrambled genes, complex morphogenesis, 'walks' and also really cute!

3. Saccinobaculus (oxymonad) -- It moves by thrashing around it's internal bundle of microtubules (axostyle), inside itself. Snake-in-a-bag. See clip in this post

4a. Myxomycetes -- plasmodial slime moulds. Although to be honest, they can easily compete with Dicty[ostelium; a cellular slime mould], but something about a large multinucleate-yet-unicellular thing of bright goop is just awesome, despite having seen plenty of

4b. Phaeodarians -- (couldn't pick between these two) Go to Coelodiceras. Now, imagine the living organism -- a giant spikey ball of axopodia, sucking in and devouring anything they can touch, including small metazoans (eg. copepods). Oh, did I mention this thing is unicellular, and uninucleate? And big?

5. Arabidopsis -- It feeds me and pays my bills. Also, I'm still a cell/developmental biologist, I swear!

Now what are yours?

Latest in bizzare intestinal ciliates: Troglocorys cava of chimps

Ahhh, I always get excited whenever something new pops up in J Euk Microbiol!

This time we have a rather bizzare entodiniomorphid ciliate (remember Litostomatea?): Troglocorys cava, a gut denizen of chimps from Uganda! The following SEM may give you the impression that it's gut has been sliced open with entrails hanging out:

Litostomatean intestinal ciliate Troglocorys from the chimp. Note the peculiar concavity (1; CO), filled with "round projections" and a "deep groove" (3; arrows). Scalebar = 10um. (Tokiwa et al. 2010 JEM)

This particular ciliate wasn't actually gutted by a microscopist, but has a rather intense concavity, shaped much like an ice cream scoop. Why? Hell if I know -- its 'mouth' (vestibulum, cytostome, etc) is actually on the top, not in the concavity, although perhaps it could employ the concavity to aid with current formation or filtering or something. Or maybe some form of endocytosis happens on that surface, kind of like on the surface of Saccinobaculus. It's a species description paper, so the emphasis really wasn't on what it actually does with its peculiar morphology. Ie, I don't know. But it definitely requires a nice diagram to show what's going on:

12 - ventral side view*; 13 - detail of left concavity (CO); 14,15 - diagram of ciliature (arrangement of cilia) on ventral (14) and (15) left sides. CV - contractile vacuole; CP - cytoproct ('anus'); MA, MI - macronucleus and micronucleus, respectively; DG - deep groove;PR - "small round projection"; VS - vestibulum (entrance to its 'mouth') Scalebar - 10um (Tokiwa et al. 2010 JEM)
*in ciliates, the ventral side is defined as the one containing the oral apparatus

Why Troglocorys? Rather aptly named:

"Troglocorys is named after the left concavity and the frontal lobe (Gr. troglo-. trogle, hole; Gr. corys, helmet)" (Tokiwa et al. 2010 JEM)

Someone could sell these as character designs for space travel sci-fi movies... imagine this thing but human-sized! Don't you wish you could enlarge some of these things and play with them? Ciliates would make such awesome (and dangerous) pets! I can't be the only person who thinks about such things...hello? *chirp chirp*

Reference:
TOKIWA, T., MODR�, D., ITO, A., POMAJB�KOV�, K., PETRŽELKOV�, K., & IMAI, S. (2010). A New Entodiniomorphid Ciliate, Troglocorys cava n. g., n. sp., from the Wild Eastern Chimpanzee from Uganda
Journal of Eukaryotic Microbiology DOI: 10.1111/j.1550-7408.2009.00456.x

Sunday Protist - Kofoidia: Crowned by luriculae

This one will be short, as I still haven't had the chance to sit down and go on an epic research blogging adventure. Let's glance at Kofoidia, an obscure hypermastigote parabasalian.

It must think it's an Oligotrich ciliate of some sort. Poor deluded thing. Since I seem to gravitate towards obscure organisms mentioned in a single paper in all the literature available/mentioned online, there is but a sole lonely drawing of this organism:

Parabasalid Kofoidia loriculata. Desperately in need of an SEM. Wood-eating gut endosymbiont from the Californian termite Kalotermes simplicicornis. Quick paper, anyone? (Light 1927 in Dogiel 1965 General Protozoology)

Unfortunately, I can't access the original Light 1927 paper (and ordering it may take a while...), so I'm gonna have to resort to scraps of information from Dogiel's 1965 General Protozoology, Adl et al. 2005 JEM and Kofoidia's Micro*scope page here.

So why did I randomly mention oligotrichs in the beginning? Superficially, hypermastigote parabasalia share quite a few features with ciliates. In fact, they're often described as 'slow-motion ciliates', as if they've been immersed in glycerol. Hypermastigote parabasalians, like ciliates, are covered in hundreds, sometimes even thousands, of flagella, as in this awesome Trichonympha SEM. However, unlike ciliates, they have a very different flagellar root structure, nuclear organisation (ciliates are weirder, probably), cellular organisation and the presence of 'parabasal fibres', for which the group is named. Furthermore, unlike most ciliates, Parabasalians are anaerobes, and lack conventional mitochondria, but rather possess hydrogen-generating hydrogenosomes (mentioned again here and here).

Trichonympha, a represenative hypermastigote, relative of Kofoidia. 40x DIC, mine.

While quite different and phylogenetically distant (excavates vs. alveolates), ciliates and hypermastigotes (the 'ciliated' parabasalia) so have some interesting cases of convergence. For one thing, both groups have representatives inhabiting various guts as commensals (or parasites), and in those cases, the organisms tend to be teeming with endosymbionts. Although considering how huge both of them are, it's not too suprising that even the free-living represenatives of both groups tend to attract tenants. As far as I know, next to nothing is known about parabasalian genome structure, so I can't really say much there, although obviously they lack the nuclear dimorphism the ciliates are famous for. One thing that I found particularly interesting in this example is the analogy to cirri, which are bundles of cilia found in many oxytrich ciliates, and often used for 'walking'. Kofoidia has tufts of flagella (same thing as cilia) bundled together into what Light 1927 termed 'loriculae', analogous to cirri!

These loriculae are arraged in a spiral (about 8-16 of then) and contain about thirty fairly long flagella (cirri tend to be shorter). These flagella seem bound lengthwise all the way to their tips, but fall apart upon fixation (the method of fixation isn't described). These bundles of flagella contract consecutively from left to right, as opposed to beating synchronously. (all from Dogiel 1965)

It's probably a very small thing, but somehow that jumped at me, that perhaps bundling up of flagella isn't so weird after all, as it first seems in ciliates. I wish more was known about this organism, including whether it may have any particular use for the 'loriculate' flagella, considering its termite gut commensal lifestyle. Cirri/loriculae make sense in benthic organisms (like many hypotrichs), since they obviously have a use for 'walking'. I don't know whether the term benthic is even applicable to gut endosymbionts...weird. Interestingly, the mastigont (flagellar root) systems form de novo upon cell division (micro*scope).

But probably what really jumped at me here is even more superficial -- this thing would look HAWT in SEM. Someone really needs to isolate and image Kofoidia!


It would be interesting to compare mechanisms of cytotaxis/cortical inheritance and patterning between ciliates, opalinids, parabasalians, Stephanopogon, etc., and see whether the principles are conserved (as one would expect), or if there may be different ways of regulating and inheriting cortical structure. Interestingly, all these ciliated looking things are bikonts, with unikonts exhibiting a much simpler cortical strcuture, at least in terms of flagella and basal bodies. Or so it seems at the moment. It seems that parabasalia have some basal body systems that form de novo, and some that are patterned in directed manner based on the remaining basal bodies (Adl et al. 2005 JEM). Hmmm, I've just found myself some more homework. Comparing cortical inheritance in parabasalia, opalinids and ciliates...

Dogiel 1965 turns out the be a wonderful source of tantalising organisms mentioned about ONCE in the distant past, and never looked at again. It's intriguing and annoying at the same time. Also, they actually paid attention to cell structure back then, which makes many of the old protozoology books a pleasure to look at and read. Even despite the systematic mess...

References:
ADL, S., SIMPSON, A., FARMER, M., ANDERSEN, R., ANDERSON, O., BARTA, J., BOWSER, S., BRUGEROLLE, G., FENSOME, R., FREDERICQ, S., JAMES, T., KARPOV, S., KUGRENS, P., KRUG, J., LANE, C., LEWIS, L., LODGE, J., LYNN, D., MANN, D., MCCOURT, R., MENDOZA, L., MOESTRUP, O., MOZLEY-STANDRIDGE, S., NERAD, T., SHEARER, C., SMIRNOV, A., SPIEGEL, F., & TAYLOR, M. (2005). The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists The Journal of Eukaryotic Microbiology, 52 (5), 399-451 DOI: 10.1111/j.1550-7408.2005.00053.x

Dogiel VA (1965) General Protozoology 2nd Ed. Oxford University Press.

Another epic TC-S quote

‘I think it best to put forward simple, detailed and specific hypotheses, since these have a better chance of stimulating (and being refuted or corroborated by) future research than are vague or unnecessarily complicated ones.’ (Cavalier-Smith 1993a p. 339.) (quoting himself in TC-S 2010 Biol Lett supplementary data PAPER.) [emphasis mine]

Can't...hold...in...laughter...AHAHAHAAAA!!

I'm gonna have to do a live blogging of a reading from the Book of Tom someday. I think that would be epic entertainment!

For those who are confused, may I refer you to:

Simple! (TC-S, 2006 Biol Direct; open access)

Disclaimer: Again, for those 'out of the loop' (so lucky...), this is not an attack against Cavalier-Smith or anything. If I didn't find his stuff interesting and worthwhile, I wouldn't be reading it in the first place. Just sayin', in case someone randomly scolds me for being mean to Tom. Which in itself is a rather humorous concept...


Speaking of which, lemme crudely summarise what the latest TC-S "Eozoa crisis" is about in a couple trees:

Note the Excavates (Euglenozoa+Percolozoa+Metamonads). Left image based on TC-S 2009 JEM(free access), right image on TC-S 2010 Biol. Lett.; some taxa translated to terms people actually use. And yes, I was having too much fun with phylo software again, this time TreeView...

Basically, Tom apparently now thinks the root of Eukarya is in the bikonts, more specifically: between Euglenozoa (eg. Euglena, Trypanosomes) and the rest of Eukaryotes. He renames Excavata to Eozoa, and all other eukaryotes to Neozoa. Some other shit happens, but basically he thinks Euglenozoans are too special. However, it is their 'derivedness' that kind of worries me there -- more special != outgroup (of course he knows that), and perhaps all other things equal, rare 'weirder' things are less likely to be basal than more 'normal' things.

What bugs me here is that he actually MAKES SENSE. This hypothesis is utterly bizzare, strange and absurd. But on the other hand...reading more about it...it might not be. Grrr. This is the main problem with Tom: he says ridiculous things, but throws out some pretty complicated and substantial evidence that takes considerable effort to reject. Even when he's obviously wrong (and probably knows it too). Thus, unlike the low-grade crazies that put out shitty hypotheses that you can throw out in a second and ignore, Tom's craziness is quality. It takes effort to deal with, and a very worthwhile effort.

Until you do a word count on one of his papers (eg. TC-S 2006 Biol Direct) and find out it to be 40K words. Holy shit.

I'll cover this in more detail once the dust in my head settles a little, and once I can slowly start rebuilding my understanding of early eukaryotic evolution after this massive blow. What a way to start off a new year!


PS: Off topic, but go check out this amazingly well-written newspaper article on dinoflagellates -- I'm impressed with the quality of research the author has done! Seldom seen in popular science writing these days...

Inching my way to the dark side...

I just dropped Gene Regulation in Development. In favour of Phylogenetic Biology.

And I call myself a [future(?)] developmental cell biologist. Heh.

You see, it's not that I ever intend to hang out for hours on end aligning sequences and building trees. I'm a proud microscopist, and will not stoop to dealing with mere gene fragments of organisms =P But...but...I'm getting tainted. My previously pure spirit is being contaminated by this...this interest...in evolution and phylogenetic thinking! For that I blame some of my friends. And also some of my instructors. And also the medically-oriented teaching on the 'other' side (eg developmental biology).

In the end, I figured that a 'good' (for my taste) phylogenetics course might actually be a better, and more useful, experience than a mediocre (again, for my taste) course in development or cell biology or genetics, even though those fields are more relevant. And considering that it becomes harder and harder to just stick to a single organism when learning about various cellular processes, I might as well just study those subjects on my own, as I prefer. It's very difficult when a course approaches a subject in a very different way from what you're looking for; eg. stressing the biomedical applications while ignoring greater diversity. I understand that pretty much every single other student in the class could care less about diversity and is perhaps utterly fascinated by biomed (and being employable), but I'm not one of them. Thus, I should probably avoid studying with them. Besides, actually knowing how to interpret phylogenies properly would never harm. Especially since few people outside evolutionary biology actually bother to learn about it...

Besides, skipping out on the opportunity to learn phylogenetics from one of its gods would be kind of stupid.

Also, I have cruel friends:

Brainwashing by evolutionary biologists, exhibit A: Opisthokont's contribution. Un-nice person sent me phylo software to play with. For fun. Did you know I had a biochem final to study for at that time? Furthermore, did you know that the biochem final randomly featured a sequence alignment question meant to 'stump' the noobs unfamiliar students? Did you know I totally aced that question and chewed them out for rooting the tree at the longest branch? (the sequences were all hypothetical, and no outgroup was specified).
There MUST be some cosmic connection there!

Evolutionary cell biology. That's a field with like, what, 4 labs, if that? Unemployment, here I come!

Goddammit, why can't I just become fascinated with cancer or something? Grrr.

Apologies for the slow posting lately -- kind of swamped with stuff. Real Life^TM tends to happen at the most inopportune moments, like when you've got a few weeks of blogging to catch up on. And delinquent posting obligations...

Less-crappy blogging to follow soon...

Mystery Micrograph #12

They're back! You probably know the drill by now...

To be referenced later; bar = 10um

Tantalising deep sea diversity...

I don't think I'd ever be able to work on a large-scale environmental genomics project -- the mere idea of having nothing but a GenBANK accession number with a fragment of ribosomal DNA for an organism really REALLY bugs me. Don't get me wrong: it's valuable data suggesting how much unseen diversity there may actually be, but this is exactly what bugs me about it -- It's simply tantalising. It's there, we can see it, but you may never encounter these mysterious organisms again. All we have for them is a tiny fragment of a sequence, and based on that, a prediction of what the organism may be related to. It's captivating and irritating at the same time.

In the latest PNAS issue, we've got one such case for a group of organisms that is particularly intriguing: deep sea protists. While drooling over those awesome diagrams of freakish deep sea fishes and reading about the metabolic madness of resident prokaryotes, one can't help but wonder just how freakish the protists must be as well, considering they're crazy enough at 1atm. Trees like this must leave one speechless; note all the numbers indicating organisms of which we just know a tiny fragment of DNA, and nothing else:

Note entire clades containing nothing but undescribed organisms. Red long-dashed lines indicate 'orphaned' organisms devoid of close relatives in GenBANK (at an arbitrary threshold). Near Perkinsus we've got a whole sea of basal alveolates. Arrow indicates position of Euglenozoa (removed due to excessively long branches). (Scheckenbach et al. 2009 PNAS)

(Some of the branchings seem kinda fishy though... ciliates branching with choanos and parts of Hacrobia? Rest of Alveolates+Haptos branching with Excavates prior to Heterokonts? Meh. This is apparently an SSU rDNA tree, and Alveolates are almost always monophyletic in SSU trees. However, considering the swaths of utterly unknown phyla there, perhaps it's not too surprising that the tree may be messed up. But then again, that's not really the point of this particular tree...)

They note a large diversity in predominantly parasitic clades, although whether these mystery organisms themselves are parasites remains a question. The stuff near Perkinsus is really interesting -- perhaps some may come in handy for understanding dinoflagellate and "proto-alveolate" (pardon my paraphyly) evolution. Now to take a look at the Euglenozoan clade:

Euglenozoan part of the tree. (Scheckenbach et al. 2009 PNAS)

Remember Diplonemids? An enigmatic apparently 'species-poor' group sister to Kinetoplastids? Judging from the tree above, we must be seriously missing something! I am perplexed by the lack of Euglenids, although perhaps they just didn't bother with Euglenid-specific primers, or maybe deep sea Euglenids are actually that rare. They do seem to be more of a freshwater group, though there are marine representatives as well. Interesting...

Hopefully at least some of these mysterious organisms will resurface again someday, and be properly described, classified and perhaps even brought into culture! One cannot help but imagine how beneath some of these GenBANK accession numbers may lurk landmark findings shedding light on some mysteries of evolutionary and developmental biology. After all, there is more to an organism than a fragment of rDNA!

Scheckenbach, F., Hausmann, K., Wylezich, C., Weitere, M., & Arndt, H. (2009). Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor Proceedings of the National Academy of Sciences, 107 (1), 115-120 DOI: 10.1073/pnas.0908816106